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The crystal structure of peptidoglycan peptidase in complex with inhibitor 2
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 acetate: acetic acid pH 4.5 and 0.8 M NaH2PO4/1.2 M K2HPO4
Crystal Properties Matthews coefficient Solvent content 3.72 66.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.175 α = 90 b = 115.175 β = 90 c = 55.34 γ = 120
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 2020-04-14 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) 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 1.8 48.403 100 0.048 0.051 1 29.48 10.595 38961 35.238
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 100 0.541 0.568 0.945 4.33 10.84
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 1.8 48.403 37012 1948 99.98 0.1569 0.1554 0.1671 0.1871 0.1949 RANDOM 34.931
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.9 r_dihedral_angle_4_deg 16.584 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_1_deg 6.395 r_angle_refined_deg 2.437 r_angle_other_deg 1.048 r_chiral_restr 0.161 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.9 r_dihedral_angle_4_deg 16.584 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_1_deg 6.395 r_angle_refined_deg 2.437 r_angle_other_deg 1.048 r_chiral_restr 0.161 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2014 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 29
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing