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The crystal structure of peptidoglycan peptidase in complex with inhibitor 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% PEG 1,000
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.441 α = 90 b = 91.037 β = 90 c = 100.877 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 100 PIXEL DECTRIS EIGER X 9M 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9796 PAL/PLS 5C (4A)
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 2.65 70 99.8 0.184 0.192 0.054 5.1 12.3 15653
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 2.65 2.7 98.4 0.948 0.998 0.303 0.92 10.3
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 (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 6JMZ 2.65 67.58 13879 728 93.03 0.2107 0.2073 0.2131 0.278 0.2746 RANDOM 45.936
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] 0.64 0.11 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.584 r_dihedral_angle_3_deg 19.218 r_dihedral_angle_4_deg 17.729 r_dihedral_angle_1_deg 6.607 r_angle_refined_deg 1.431 r_angle_other_deg 0.976 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.584 r_dihedral_angle_3_deg 19.218 r_dihedral_angle_4_deg 17.729 r_dihedral_angle_1_deg 6.607 r_angle_refined_deg 1.431 r_angle_other_deg 0.976 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3994 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing