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Crystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the imipenem-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MKA PBP5 apo open
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 0.1 M trisodium citrate, 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 6 79.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.933 α = 90 b = 192.933 β = 90 c = 155.86 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 Adjustable focus K-B pair Si plus Pt, Rh coatings 2016-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03320 APS 23-ID-D
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 2.8 29.84 99.8 0.157 0.166 0.052 0.999 20.1 18.3 42442 66.51
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 2.8 2.91 98.5 1.661 1.803 0.678 0.337 1.8 12.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PBP5 apo open 2.8 29.84 1.34 42395 2108 99.72 0.174 0.1727 0.1985 0.1838
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 16.434 f_angle_d 0.494 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4782 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing