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Crystal structure of Prc with S452I and L252Y mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 PEG3350, sodium thyocinate
Crystal Properties Matthews coefficient Solvent content 3.68 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.277 α = 90 b = 129.277 β = 90 c = 236.566 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300HE Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , Toroidal Focusing Mirror 2018-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.42 50 99.4 0.075 0.145 0.069 13.8 4.3 31494 44.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.42 3.54 100 0.651 0.942 0.446 0.772 2.1 4.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WQL 3.42 29.97 27244 1515 90.87 0.24193 0.23941 0.244 0.28758 0.2862 RANDOM 71.348
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_long_range_B_refined 25.931 r_long_range_B_other 25.931 r_dihedral_angle_4_deg 23.177 r_dihedral_angle_3_deg 17.799 r_mcangle_it 13.074 r_mcangle_other 13.073 r_scangle_other 12.607 r_dihedral_angle_1_deg 8.454 r_mcbond_it 8.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_long_range_B_refined 25.931 r_long_range_B_other 25.931 r_dihedral_angle_4_deg 23.177 r_dihedral_angle_3_deg 17.799 r_mcangle_it 13.074 r_mcangle_other 13.073 r_scangle_other 12.607 r_dihedral_angle_1_deg 8.454 r_mcbond_it 8.281 r_mcbond_other 8.281 r_scbond_it 7.966 r_scbond_other 7.964 r_angle_refined_deg 1.788 r_angle_other_deg 0.948 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10143 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing Coot model building HKL-2000 data reduction