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The crystal structure of peptidoglycan peptidase in complex with inhibitor 3-1
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 3.85 68.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.41 α = 90 b = 115.41 β = 90 c = 56.99 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 2.84 28.85 99.7 0.143 0.159 0.992 8.55 5.317 19937 61.697
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 2.84 3.01 99 0.897 0.994 0.682 1.39 5.371
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 2.84 28.85 9852 519 99.89 0.2147 0.2133 0.2125 0.2412 0.2399 RANDOM 70.165
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] -0.56 -0.28 -0.56 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_3_deg 17.405 r_dihedral_angle_4_deg 8.628 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 0.986 r_angle_other_deg 0.621 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_3_deg 17.405 r_dihedral_angle_4_deg 8.628 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 0.986 r_angle_other_deg 0.621 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2014 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing