data for structural and crystallization communications - example

Example: refinement

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
No. of solvent atoms 41
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



Follow Acta Cryst. F
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds