|
Based in part on Rehse, P. H. & Tahirov, T. H. (2005).
Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.
Acta Cryst. D61, 1207-1212.
[1VDX
].
In this example of the structure of a putative 2'-5' RNA ligase
there is a single molecule in the asymmetric unit, and no
non-crystallographic symmetry restraints are imposed.
Example 1: a putative 2'-5' RNA ligase
# Model generation and refinement
_computing.structure_refinement 'CNS (Brunger et al., 1998)'
_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 39.84
_refine.ls_d_res_high 2.40
_refine_ls_shell.d_res_low 2.55
_refine_ls_shell.d_res_high 2.40
_refine.ls_number_reflns_R_work 7386
_refine_ls_shell.number_reflns_R_work 1045
_refine.ls_number_reflns_obs 7386
_refine_ls_shell.number_reflns_obs ?
_refine.ls_R_factor_obs 0.225
_refine_ls_shell.R_factor_obs ?
_refine_B_iso.treatment isotropic
_refine_B_iso.class 'all'
_refine.B_iso_mean 43.5
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine_hist.pdbx_number_atoms_protein 1488
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 1
_refine_hist.number_atoms_solvent 41
_refine_hist.number_atoms_total 1530
_refine.ls_number_parameters 6126
_refine_ls_restr_ncs.ncs_model_details 'none, one molecule per a.u.'
_refine.solvent_model_param_bsol 40.3079
_refine.solvent_model_param_ksol 0.344613
_refine.solvent_model_details 'flat model'
# Model validation
_refine.ls_R_factor_R_work 0.225
_refine_ls_shell.R_factor_R_work 0.277
_refine.ls_number_reflns_R_free 552
_refine_ls_shell.number_reflns_R_free 83
_refine.ls_R_factor_R_free 0.274
_refine_ls_shell.R_factor_R_free 0.326
_refine.overall_SU_R_Cruickshank_DPI 0.35
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.number
c_bond_d 0.007 0.010 1456
c_angle_deg 1.40 1.50 2004
c_dihedral_angle_d 22.9 ? ?
c_improper_angle_d 0.91 ? ?
c_mcbond_it 3.29 1.50 ?
c_mcangle_it 4.80 2.00 ?
c_scbond_it 5.24 2.00 ?
c_scangle_it 7.13 2.50 ?
How this example will appear in the journal
|
| Table 3. Model generation and refinement
|
| Values for the outer shell are given in parentheses.
|
|
|
|
| Software used
|
CNS (Brünger et al., 1998)
|
| Refinement on
|
F
|
| σ cutoff
|
F > 0.0σ(F)
|
| Resolution range (Å)
|
39.84-2.40 (2.55-2.40)
|
| No. of reflections used in refinement
|
7386 (1045)
|
| No. of reflections above σ cutoff in final cycle
|
7386
|
| Final overall R factor
|
0.225
|
| Atomic displacement model
|
Isotropic
|
| Overall average B factor (Å2)
|
43.5
|
| No. of protein atoms
|
1488
|
| No. of ligand atoms
|
1
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| No. of solvent atoms
|
41
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| Total No. of atoms
|
1530
|
| No. of refined parameters
|
6126
|
| Bulk solvent model
|
Flat model; BSOL = 40.31,
KSOL = 0.347
|
|
| Table 4. Model validation
|
| Values for the outer shell are given in parentheses.
|
|
|
|
| Final Rwork
|
0.225 (0.277)
|
| No. of reflections for Rfree
|
552 (83)
|
| Final Rfree
|
0.274 (0.326)
|
| Cruickshank DPI
|
0.35
|
|
|
|
|
|
|
|
|
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