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Crystal structure of Prc with S452I and L252Y mutations in complex with NlpI
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, HANGING DROP 8 295 PEG3350, Calcium acetate, Imidazole
Crystal Properties Matthews coefficient Solvent content 2.95 58.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.936 α = 90 b = 143.882 β = 90 c = 153.599 γ = 90
Symmetry Space Group P 21 21 21
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 LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors 2017-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
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 2.8 30 98.3 0.102 0.154 0.055 13.92 7.9 64129 38.87
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 2.8 2.9 99.4 0.615 0.748 0.263 0.895 3.3 6.9
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 2.8 29.98 60219 3248 96.84 0.22442 0.2215 0.224 0.27769 0.2752 RANDOM 56.008
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_4_deg 19.576 r_dihedral_angle_3_deg 18.349 r_long_range_B_refined 14.686 r_long_range_B_other 14.686 r_mcangle_it 9.911 r_mcangle_other 9.91 r_scangle_other 9.571 r_dihedral_angle_1_deg 7.045 r_mcbond_it 6.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_4_deg 19.576 r_dihedral_angle_3_deg 18.349 r_long_range_B_refined 14.686 r_long_range_B_other 14.686 r_mcangle_it 9.911 r_mcangle_other 9.91 r_scangle_other 9.571 r_dihedral_angle_1_deg 7.045 r_mcbond_it 6.617 r_mcbond_other 6.616 r_scbond_it 6.258 r_scbond_other 6.258 r_angle_refined_deg 1.888 r_angle_other_deg 1.35 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 14407 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection Coot model building PHASER phasing HKL-2000 data reduction HKL-2000 data scaling