2-Azido-(R)-3,5-O-benzyl­idene-2-de­oxy-2-C-methyl-D-xylono-1,4-lactone [(2S,4aR,7R,7aR)-7-azido-7-methyl-2-phenyl­dihydro-4H-furo[3,2-d][1,3]dioxin-6(4aH)-one]

Hotchkiss, D.J.; Jenkinson, S.F.; Booth, K.V.; Fleet, G.W.J.; Watkin, D.J.

doi:10.1107/S1600536807014560

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2-Azido-(R)-3,5-O-benzylidene-2-deoxy-2-C-methyl-D-xylono-1,4-lactone [(2S,4aR,7R,7aR)-7-azido-7-methyl-2-phenyldihydro-4H-furo[3,2-d][1,3]dioxin-6(4aH)-one]

D. J. Hotchkiss, S. F. Jenkinson, K. V. Booth, G. W. J. Fleet and D. J. Watkin

The unknown relative configurations in the title compound, C₁₃H₁₃N₃O₄, of the acetal carbon and of the quaternary carbon bearing the azide were determined by X-ray crystallographic analysis; the absolute configuration was defined by the use of 2-C-methyl-D-lyxonolactone as a starting material. There are two molecules in the asymmetric unit (Z' = 2).

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807014560/lh2348sup1.cif Contains datablocks 5, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807014560/lh23485sup2.hkl Contains datablock 5

CCDC reference: 647274

checkCIF report

Key indicators

Single-crystal X-ray study
T = 150 K
Mean (C-C) = 0.005 Å
R factor = 0.044
wR factor = 0.119
Data-to-parameter ratio = 9.3

checkCIF/PLATON results

No syntax errors found



Alert level B
ABSTM02_ALERT_3_B  The ratio of expected to reported Tmax/Tmin(RR') is < 0.75
            Tmin and Tmax reported:      0.690     0.990
            Tmin(prime) and Tmax expected:      0.959     0.990
            RR(prime) =      0.720
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large .............       0.72
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C101   -   C102    ..       9.44 su

Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.96
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N117   -   N118    ..       6.49 su
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........         13

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.56
           From the CIF: _reflns_number_total               3360
           Count of symmetry unique reflns         3507
           Completeness (_total/calc)             95.81%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C101   = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C102   = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C103   = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C109   = .          R

   0 ALERT level A = In general: serious problem
   3 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   9 ALERT level G = General alerts; check

   8 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

2-Azido-(R)-3,5-O-benzylidene-2-deoxy-2-C-methyl-D-xylono- 1,4-lactone top

Crystal data top

C₁₃H₁₃N₃O₄	D_x = 1.362 Mg m⁻³
M_r = 275.26	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 3025 reflections
a = 9.7507 (2) Å	θ = 5–27°
b = 10.4263 (2) Å	µ = 0.10 mm⁻¹
c = 26.4090 (5) Å	T = 150 K
V = 2684.84 (9) Å³	Plate, colourless
Z = 8	0.40 × 0.40 × 0.10 mm
F(000) = 1152

Data collection top

Nonius KappaCCD diffractometer	2414 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.055
ω scans	θ_max = 27.6°, θ_min = 5.4°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −12→12
T_min = 0.69, T_max = 0.99	k = −13→13
12730 measured reflections	l = −33→33
3360 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.044	w = 1/[σ²(F²) + (0.05P)² + 0.85P], where P = [max(F_o²,0) + 2F_c²]/3
wR(F²) = 0.119	(Δ/σ)_max = 0.004
S = 0.87	Δρ_max = 0.21 e Å⁻³
3360 reflections	Δρ_min = −0.18 e Å⁻³
362 parameters	Extinction correction: Larson (1970), Equation 22
0 restraints	Extinction coefficient: 3314.893
Primary atom site location: structure-invariant direct methods

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.5922 (3)	0.8368 (3)	0.56501 (11)	0.0587
C2	0.5707 (3)	0.9098 (3)	0.61377 (10)	0.0561
C3	0.6465 (4)	0.8273 (3)	0.65218 (12)	0.0678
O4	0.7600 (2)	0.7754 (2)	0.62420 (11)	0.0772
C5	0.7332 (4)	0.7793 (3)	0.57437 (16)	0.0730
O6	0.8099 (3)	0.7366 (3)	0.54353 (13)	0.1168
C7	0.6988 (4)	0.9014 (4)	0.69740 (13)	0.0858
O8	0.7623 (3)	1.0189 (2)	0.68232 (9)	0.0773
C9	0.6731 (3)	1.0924 (3)	0.65274 (11)	0.0657
O10	0.6413 (2)	1.02832 (17)	0.60689 (7)	0.0587
C11	0.7403 (3)	1.2162 (3)	0.63730 (11)	0.0605
C12	0.8701 (4)	1.2159 (3)	0.61683 (14)	0.0773
C13	0.9269 (4)	1.3299 (4)	0.59981 (16)	0.0889
C14	0.8560 (5)	1.4413 (3)	0.60341 (14)	0.0820
C15	0.7279 (5)	1.4435 (3)	0.62384 (14)	0.0815
C16	0.6693 (4)	1.3296 (3)	0.64103 (13)	0.0730
N17	0.4943 (3)	0.7264 (3)	0.56741 (11)	0.0746
N18	0.5080 (3)	0.6487 (3)	0.53294 (12)	0.0788
N19	0.5098 (5)	0.5715 (3)	0.50353 (16)	0.1136
C20	0.5793 (4)	0.9114 (3)	0.51646 (12)	0.0809
C101	0.6629 (3)	0.7650 (4)	0.32312 (11)	0.0695
C102	0.6434 (3)	0.6251 (3)	0.30903 (11)	0.0644
C103	0.7301 (3)	0.6110 (3)	0.26204 (11)	0.0691
O104	0.8458 (2)	0.6983 (2)	0.27092 (8)	0.0741
C105	0.8083 (3)	0.7894 (4)	0.30301 (12)	0.0685
O106	0.8806 (3)	0.8814 (3)	0.31213 (10)	0.0875
C107	0.7839 (4)	0.4766 (3)	0.25344 (12)	0.0770
O108	0.8227 (2)	0.4155 (2)	0.29978 (8)	0.0747
C109	0.7161 (3)	0.4192 (3)	0.33539 (12)	0.0691
O110	0.6941 (2)	0.5511 (2)	0.34969 (7)	0.0664
C111	0.7527 (3)	0.3440 (3)	0.38141 (13)	0.0695
C116	0.8045 (4)	0.2209 (4)	0.37538 (16)	0.0844
C115	0.8351 (5)	0.1477 (4)	0.41721 (19)	0.1012
C114	0.8173 (5)	0.1959 (4)	0.46476 (17)	0.0989
C113	0.7642 (6)	0.3152 (4)	0.47084 (16)	0.1051
C112	0.7319 (5)	0.3903 (4)	0.42933 (14)	0.0906
N117	0.5679 (3)	0.8365 (4)	0.28986 (11)	0.0815
N118	0.5814 (3)	0.9550 (4)	0.29177 (10)	0.0796
N119	0.5821 (4)	1.0637 (4)	0.29062 (12)	0.1016
C120	0.6465 (4)	0.8011 (4)	0.37851 (12)	0.0776
H21	0.4741	0.9199	0.6221	0.0658*
H31	0.5940	0.7550	0.6648	0.0809*
H71	0.7706	0.8514	0.7152	0.1037*
H72	0.6182	0.9217	0.7198	0.1045*
H91	0.5842	1.1104	0.6707	0.0789*
H121	0.9171	1.1383	0.6143	0.0935*
H131	1.0154	1.3271	0.5855	0.1069*
H141	0.8969	1.5187	0.5918	0.0985*
H151	0.6787	1.5203	0.6261	0.0978*
H161	0.5800	1.3332	0.6553	0.0884*
H201	0.6083	0.8589	0.4879	0.1217*
H202	0.6380	0.9880	0.5178	0.1212*
H203	0.4848	0.9373	0.5112	0.1222*
H1021	0.5516	0.6024	0.3024	0.0768*
H1031	0.6771	0.6374	0.2322	0.0815*
H1071	0.8613	0.4820	0.2307	0.0908*
H1072	0.7100	0.4193	0.2379	0.0914*
H1091	0.6333	0.3851	0.3183	0.0818*
H1161	0.8174	0.1913	0.3422	0.1018*
H1151	0.8672	0.0631	0.4129	0.1223*
H1141	0.8405	0.1462	0.4930	0.1191*
H1131	0.7493	0.3474	0.5033	0.1267*
H1121	0.6969	0.4710	0.4341	0.1089*
H1201	0.6577	0.8914	0.3832	0.1147*
H1202	0.7147	0.7560	0.3974	0.1157*
H1203	0.5552	0.7754	0.3888	0.1147*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0539 (15)	0.0523 (14)	0.0699 (17)	−0.0124 (13)	0.0065 (14)	0.0002 (13)
C2	0.0420 (12)	0.0570 (14)	0.0692 (16)	−0.0023 (12)	−0.0017 (13)	0.0013 (13)
C3	0.0609 (18)	0.0652 (17)	0.077 (2)	−0.0134 (17)	−0.0018 (17)	0.0156 (15)
O4	0.0562 (12)	0.0658 (12)	0.1094 (19)	0.0086 (11)	−0.0037 (13)	0.0168 (12)
C5	0.0623 (18)	0.0553 (16)	0.102 (3)	−0.0013 (16)	0.020 (2)	0.0039 (17)
O6	0.097 (2)	0.104 (2)	0.149 (2)	0.0185 (18)	0.052 (2)	−0.0073 (19)
C7	0.098 (3)	0.084 (2)	0.076 (2)	−0.031 (2)	−0.0217 (19)	0.0187 (18)
O8	0.0803 (14)	0.0738 (13)	0.0777 (13)	−0.0157 (12)	−0.0247 (12)	0.0142 (11)
C9	0.0596 (17)	0.0708 (17)	0.0667 (17)	−0.0052 (16)	−0.0066 (15)	−0.0061 (15)
O10	0.0578 (10)	0.0500 (9)	0.0684 (11)	−0.0051 (9)	−0.0075 (10)	0.0019 (8)
C11	0.0613 (18)	0.0578 (15)	0.0624 (17)	−0.0065 (15)	−0.0111 (14)	−0.0018 (13)
C12	0.0623 (19)	0.0655 (17)	0.104 (2)	0.0016 (16)	−0.0079 (19)	0.0046 (18)
C13	0.067 (2)	0.083 (2)	0.116 (3)	−0.021 (2)	−0.010 (2)	0.017 (2)
C14	0.094 (3)	0.0656 (19)	0.087 (2)	−0.017 (2)	−0.026 (2)	0.0122 (17)
C15	0.101 (3)	0.0592 (17)	0.084 (2)	0.0007 (19)	−0.014 (2)	0.0024 (16)
C16	0.076 (2)	0.0693 (18)	0.0735 (19)	0.0037 (18)	−0.0024 (18)	−0.0053 (15)
N17	0.0781 (17)	0.0651 (15)	0.0807 (17)	−0.0233 (14)	0.0127 (15)	−0.0063 (14)
N18	0.090 (2)	0.0533 (14)	0.093 (2)	−0.0140 (15)	0.0023 (18)	−0.0025 (16)
N19	0.144 (3)	0.0672 (19)	0.130 (3)	−0.013 (2)	0.005 (3)	−0.019 (2)
C20	0.100 (3)	0.077 (2)	0.0656 (19)	−0.022 (2)	−0.0037 (18)	0.0055 (16)
C101	0.0459 (16)	0.104 (2)	0.0589 (16)	0.0114 (17)	−0.0042 (14)	0.0096 (17)
C102	0.0477 (15)	0.0838 (19)	0.0617 (16)	0.0024 (15)	−0.0056 (13)	0.0055 (15)
C103	0.0575 (17)	0.092 (2)	0.0577 (16)	−0.0016 (18)	−0.0023 (14)	0.0029 (16)
O104	0.0558 (12)	0.0948 (15)	0.0717 (13)	0.0013 (12)	0.0085 (11)	0.0000 (12)
C105	0.0526 (17)	0.083 (2)	0.0698 (19)	0.0054 (17)	−0.0064 (15)	0.0062 (18)
O106	0.0687 (14)	0.0952 (16)	0.0985 (17)	−0.0011 (15)	−0.0034 (13)	0.0035 (14)
C107	0.071 (2)	0.097 (2)	0.0630 (19)	0.006 (2)	−0.0007 (16)	−0.0054 (17)
O108	0.0656 (13)	0.0924 (15)	0.0661 (12)	0.0081 (12)	0.0058 (11)	−0.0002 (11)
C109	0.0541 (16)	0.079 (2)	0.074 (2)	−0.0014 (16)	−0.0027 (15)	−0.0059 (16)
O110	0.0572 (12)	0.0826 (13)	0.0595 (11)	0.0014 (11)	−0.0013 (10)	0.0037 (10)
C111	0.0553 (16)	0.0799 (19)	0.073 (2)	−0.0131 (16)	−0.0024 (16)	0.0054 (16)
C116	0.074 (2)	0.088 (2)	0.091 (2)	0.007 (2)	0.001 (2)	0.001 (2)
C115	0.090 (3)	0.096 (3)	0.119 (3)	0.009 (3)	0.003 (3)	0.018 (3)
C114	0.106 (3)	0.094 (3)	0.097 (3)	0.000 (3)	−0.007 (3)	0.021 (2)
C113	0.139 (4)	0.098 (3)	0.078 (2)	−0.006 (3)	−0.007 (3)	0.008 (2)
C112	0.115 (3)	0.084 (2)	0.073 (2)	0.003 (2)	−0.003 (2)	0.0062 (19)
N117	0.0663 (17)	0.099 (2)	0.0792 (19)	0.0223 (18)	−0.0138 (15)	0.0123 (16)
N118	0.0583 (16)	0.117 (3)	0.0630 (17)	0.0228 (19)	0.0004 (13)	0.0160 (17)
N119	0.105 (3)	0.113 (3)	0.087 (2)	0.043 (2)	0.0005 (19)	0.018 (2)
C120	0.0705 (19)	0.096 (2)	0.0661 (18)	0.018 (2)	0.0003 (17)	0.0014 (17)

Geometric parameters (Å, º) top

C1—C2	1.510 (4)	C101—C102	1.517 (5)
C1—C5	1.520 (5)	C101—C105	1.535 (5)
C1—N17	1.497 (4)	C101—N117	1.478 (4)
C1—C20	1.505 (4)	C101—C120	1.519 (4)
C2—C3	1.521 (4)	C102—C103	1.509 (4)
C2—O10	1.427 (3)	C102—O110	1.412 (3)
C2—H21	0.973	C102—H1021	0.942
C3—O4	1.437 (4)	C103—O104	1.468 (4)
C3—C7	1.511 (5)	C103—C107	1.513 (5)
C3—H31	0.970	C103—H1031	0.981
O4—C5	1.342 (5)	O104—C105	1.324 (4)
C5—O6	1.192 (4)	C105—O106	1.214 (4)
C7—O8	1.429 (4)	C107—O108	1.430 (4)
C7—H71	0.992	C107—H1071	0.965
C7—H72	1.006	C107—H1072	1.023
O8—C9	1.398 (4)	O108—C109	1.403 (4)
C9—O10	1.418 (3)	C109—O110	1.442 (4)
C9—C11	1.504 (4)	C109—C111	1.490 (5)
C9—H91	1.005	C109—H1091	0.991
C11—C12	1.376 (5)	C111—C116	1.389 (5)
C11—C16	1.374 (4)	C111—C112	1.369 (5)
C12—C13	1.386 (5)	C116—C115	1.375 (5)
C12—H121	0.932	C116—H1161	0.938
C13—C14	1.355 (5)	C115—C114	1.364 (6)
C13—H131	0.943	C115—H1151	0.943
C14—C15	1.361 (6)	C114—C113	1.356 (6)
C14—H141	0.951	C114—H1141	0.937
C15—C16	1.393 (5)	C113—C112	1.384 (5)
C15—H151	0.936	C113—H1131	0.931
C16—H161	0.950	C112—H1121	0.916
N17—N18	1.226 (4)	N117—N118	1.244 (5)
N18—N19	1.118 (4)	N118—N119	1.133 (5)
C20—H201	0.975	C120—H1201	0.956
C20—H202	0.983	C120—H1202	0.955
C20—H203	0.970	C120—H1203	0.968

C2—C1—C5	100.7 (3)	C102—C101—C105	101.0 (3)
C2—C1—N17	105.2 (2)	C102—C101—N117	105.1 (3)
C5—C1—N17	105.5 (2)	C105—C101—N117	106.8 (3)
C2—C1—C20	117.1 (2)	C102—C101—C120	117.5 (3)
C5—C1—C20	114.7 (3)	C105—C101—C120	112.9 (3)
N17—C1—C20	112.3 (3)	N117—C101—C120	112.4 (3)
C1—C2—C3	102.5 (2)	C101—C102—C103	103.0 (3)
C1—C2—O10	105.1 (2)	C101—C102—O110	107.1 (2)
C3—C2—O10	109.9 (2)	C103—C102—O110	112.1 (2)
C1—C2—H21	112.5	C101—C102—H1021	114.0
C3—C2—H21	112.3	C103—C102—H1021	110.8
O10—C2—H21	113.7	O110—C102—H1021	109.7
C2—C3—O4	104.1 (2)	C102—C103—O104	103.8 (2)
C2—C3—C7	113.7 (3)	C102—C103—C107	114.1 (3)
O4—C3—C7	109.8 (3)	O104—C103—C107	109.4 (3)
C2—C3—H31	114.4	C102—C103—H1031	109.7
O4—C3—H31	106.9	O104—C103—H1031	111.0
C7—C3—H31	107.7	C107—C103—H1031	108.8
C3—O4—C5	110.0 (3)	C103—O104—C105	109.6 (2)
C1—C5—O4	110.4 (3)	C101—C105—O104	110.9 (3)
C1—C5—O6	127.1 (4)	C101—C105—O106	126.8 (3)
O4—C5—O6	122.4 (4)	O104—C105—O106	122.2 (3)
C3—C7—O8	111.4 (3)	C103—C107—O108	112.0 (3)
C3—C7—H71	110.1	C103—C107—H1071	108.0
O8—C7—H71	106.1	O108—C107—H1071	110.6
C3—C7—H72	108.0	C103—C107—H1072	110.9
O8—C7—H72	108.8	O108—C107—H1072	105.7
H71—C7—H72	112.5	H1071—C107—H1072	109.6
C7—O8—C9	110.9 (3)	C107—O108—C109	111.4 (2)
O8—C9—O10	110.8 (2)	O108—C109—O110	108.2 (3)
O8—C9—C11	110.6 (2)	O108—C109—C111	110.8 (3)
O10—C9—C11	105.6 (2)	O110—C109—C111	108.9 (3)
O8—C9—H91	112.0	O108—C109—H1091	106.8
O10—C9—H91	107.5	O110—C109—H1091	109.9
C11—C9—H91	110.1	C111—C109—H1091	112.2
C2—O10—C9	113.9 (2)	C109—O110—C102	112.0 (2)
C9—C11—C12	120.3 (3)	C109—C111—C116	118.7 (3)
C9—C11—C16	120.0 (3)	C109—C111—C112	122.2 (3)
C12—C11—C16	119.6 (3)	C116—C111—C112	119.1 (3)
C11—C12—C13	119.5 (3)	C111—C116—C115	120.0 (4)
C11—C12—H121	118.8	C111—C116—H1161	117.3
C13—C12—H121	121.7	C115—C116—H1161	122.7
C12—C13—C14	120.6 (3)	C116—C115—C114	120.5 (4)
C12—C13—H131	118.0	C116—C115—H1151	119.6
C14—C13—H131	121.4	C114—C115—H1151	119.9
C13—C14—C15	120.7 (3)	C115—C114—C113	119.7 (4)
C13—C14—H141	119.4	C115—C114—H1141	119.9
C15—C14—H141	119.9	C113—C114—H1141	120.3
C14—C15—C16	119.4 (3)	C114—C113—C112	120.8 (4)
C14—C15—H151	120.7	C114—C113—H1131	120.0
C16—C15—H151	119.9	C112—C113—H1131	119.2
C15—C16—C11	120.2 (3)	C113—C112—C111	119.9 (4)
C15—C16—H161	118.1	C113—C112—H1121	119.8
C11—C16—H161	121.6	C111—C112—H1121	120.3
C1—N17—N18	114.1 (3)	C101—N117—N118	114.3 (3)
N17—N18—N19	173.1 (4)	N117—N118—N119	173.1 (4)
C1—C20—H201	110.2	C101—C120—H1201	111.0
C1—C20—H202	109.9	C101—C120—H1202	108.0
H201—C20—H202	108.4	H1201—C120—H1202	109.7
C1—C20—H203	110.2	C101—C120—H1203	107.4
H201—C20—H203	108.7	H1201—C120—H1203	109.9
H202—C20—H203	109.4	H1202—C120—H1203	111.0

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