|
Based in part on Kantardjieff, K. A., Vasquez, C., Castro, P., Warfel, N. M.,
Rho, B.-S., Lekin, T., Kim, C.-Y., Segelke, B. W., Terwilliger, T. C.
& Rupp, B. (2005).
Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug target.
Acta Cryst. D61, 355-364.
[1W30
].
In this example of the structure of M. tuberculosis pyR protein
there are two molecules in the asymmetric unit, and non-crystallographic
symmetry restraints are imposed.
Example 2: M. tuberculosis pyR protein
# Model generation and refinement
_computing.structure_refinement 'REFMAC 5.1.24 (Murshudov et al., 1997)'
_refine.ls_structure_factor_coef F
_refine.pdbx_ls_sigma_F 0.0
_refine.pdbx_ls_sigma_I .
_refine.pdbx_ls_sigma_Fsqd .
_refine.ls_d_res_low 30.00
_refine.ls_d_res_high 1.90
_refine_ls_shell.d_res_low 1.949
_refine_ls_shell.d_res_high 1.90
_refine.ls_number_reflns_R_work 28063
_refine_ls_shell.number_reflns_R_work 2213
_refine.ls_number_reflns_obs 30.276
_refine_ls_shell.number_reflns_obs ?
_refine.ls_R_factor_obs 0.20649
_refine_ls_shell.R_factor_obs ?
_refine_B_iso.treatment isotropic
_refine_B_iso.class 'all'
_refine.B_iso_mean 31.99
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine_hist.pdbx_number_atoms_protein 2656
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 0
_refine_hist.number_atoms_solvent 329
_refine_hist.number_atoms_total 2985
_refine.ls_number_parameters 12324
_refine_ls_restr_ncs.ncs_model_details
'two molecules per asymmetric unit, termini and 4 loops unrestrained'
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.solvent_model_details 'Babinet with mask'
_refine.pdbx_solvent_vdw_probe_radii 1.40
_refine.pdbx_solvent_ion_probe_radii 0.80
_refine.pdbx_solvent_shrinkage_radii 0.80
# Model validation
_refine.ls_R_factor_R_work 0.205
_refine_ls_shell.R_factor_R_work 0.278
_refine.ls_number_reflns_R_free 1589
_refine_ls_shell.number_reflns_R_free 116
_refine.ls_R_factor_R_free 0.244
_refine_ls_shell.R_factor_R_free 0.290
_refine.overall_SU_R_Cruickshank_DPI 0.26
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.number
r_bond_refined_d 0.020 0.021 2692
r_bond_other_d 0.002 0.020 2623
r_angle_refined_deg 1.816 1.900 3743
r_angle_other_deg 1.798 1.974 3655
r_mcbond_it 1.222 1.500 1738
r_mcangle_it 2.167 2.000 2805
r_scbond_it 2.998 3.000 954
r_scangle_it 5.167 4.500 850
How this example will appear in the journal
|
| Table 3. Structure refinement
|
| Values for the outer shell are given in parentheses.
|
|
|
|
| Software used
|
REFMAC 5.1.24 (Murshudov et al., 1997)
|
| Refinement on
|
F
|
| σ cutoff
|
F > 0.0σ(F)
|
| Resolution range (Å)
|
30.00-1.90 (1.949-1.90)
|
| No. of reflections used in refinement
|
28063 (2213)
|
| No. of reflections above σ cutoff in final cycle
|
30276
|
| Final overall R factor
|
0.206
|
| Atomic displacement model
|
Isotropic
|
| Overall average B factor (Å2)
|
31.99
|
| No. of protein atoms
|
2656
|
| No. of solvent atoms
|
329
|
| Total No. of atoms
|
2985
|
| No. of refined parameters
|
12324
|
| Bulk solvent model
|
Babinet with mask
|
|
| Table 4. Model validation
|
| Values for the outer shell are given in parentheses.
|
|
|
|
| Final Rwork
|
0.205 (0.278)
|
| No. of reflections for Rfree
|
1589 (116)
|
| Final Rfree
|
0.244 (0.290)
|
| Cruickshank DPI
|
0.26
|
|
|
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