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Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.041 α = 90 b = 109.041 β = 90 c = 105.163 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.84 109.1 89.7 0.112 0.046 0.999 13.6 12.6 9545 109.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 3.29 68.2 1.877 0.769 0.584 1.5 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6j7c 2.841 77.223 9530 542 61.432 0.256 0.2513 0.25 0.3296 0.3314 126.233
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 4.282 4.282 -8.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.879 r_dihedral_angle_3_deg 20.383 r_dihedral_angle_4_deg 13.501 r_dihedral_angle_1_deg 9.703 r_lrange_it 5.513 r_lrange_other 5.513 r_mcangle_it 2.996 r_mcangle_other 2.996 r_scangle_it 2.429 r_scangle_other 2.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.879 r_dihedral_angle_3_deg 20.383 r_dihedral_angle_4_deg 13.501 r_dihedral_angle_1_deg 9.703 r_lrange_it 5.513 r_lrange_other 5.513 r_mcangle_it 2.996 r_mcangle_other 2.996 r_scangle_it 2.429 r_scangle_other 2.429 r_mcbond_it 1.741 r_mcbond_other 1.741 r_angle_refined_deg 1.429 r_scbond_it 1.32 r_scbond_other 1.32 r_angle_other_deg 1.058 r_nbd_refined 0.223 r_nbd_other 0.201 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.166 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.058 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5172 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement xia2 data reduction STARANISO data scaling DIALS data scaling MoRDa phasing PHASER phasing