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The crystal structure of peptidoglycan peptidase in complex with inhibitor 3-3
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 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.84 67.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.649 α = 90 b = 115.649 β = 90 c = 56.614 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 2020-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0000 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 2.59 48.882 100 0.159 0.167 0.997 16.59 10.704 13306 40.006
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 2.59 2.75 100 0.591 0.62 0.973 5.96 10.904
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 2.61 33.38 12639 665 99.74 0.1726 0.1696 0.1765 0.231 0.2311 RANDOM 39.671
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] -0.02 -0.01 -0.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_3_deg 18.262 r_dihedral_angle_4_deg 14.798 r_dihedral_angle_1_deg 7.38 r_angle_refined_deg 1.814 r_angle_other_deg 0.881 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_3_deg 18.262 r_dihedral_angle_4_deg 14.798 r_dihedral_angle_1_deg 7.38 r_angle_refined_deg 1.814 r_angle_other_deg 0.881 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 31 Heterogen Atoms 22
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing