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Crystal structure of Penicillin Binding Protein 5 (PBP5) R464A variant penicillin bound form from Enterococcus faecium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.085 M Tris pH 8.0, 2.55 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 5.93 79.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.741 α = 90 b = 191.741 β = 90 c = 156.39 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS 6M 2019-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.09 39.68 99.7 0.288 0.295 0.066 0.996 13.2 19.9 31376
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 3.09 3.26 98.5 2.256 2.314 0.508 0.865 20.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6MKA 3.09 38.1 1.92 31305 2803 99.58 0.1889 0.1876 0.1883 0.2132 0.2127
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.718 f_angle_d 0.492 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4739 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing