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Crystal structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E variant apo 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 5 298 0.1 M citric acid pH 5.0, 3.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 5.94 79.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.777 α = 90 b = 192.777 β = 90 c = 155.427 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 2018-04-08 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 2.56 39.78 99.9 0.068 0.072 0.021 0.999 23.8 11.2 55258
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 2.56 2.63 99 1.139 1.193 0.352 0.739 11.2
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 2.56 39.78 1.91 55220 5202 99.87 0.1929 0.1918 0.1988 0.2136 0.2205
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 10.992 f_angle_d 0.412 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4857 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing