data for structural and crystallization communications - example

Example: refinement

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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