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Crystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 0.1 M trisodium citrate, 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 5.56 77.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.54 α = 90 b = 190.54 β = 90 c = 156.467 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 Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2016-06-23 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 2.7 39.5 98.6 0.059 0.08 0.054 0.997 13 3.1 45763 47.82
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 2.7 2.79 97.6 0.445 0.613 0.419 0.707 2.5 3.2
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 FREE R-VALUE 5DVY 2.698 39.503 1.34 45727 2261 98.34 0.1807 0.1793 0.1821 0.206 0.2055
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 6.557 f_angle_d 0.743 f_chiral_restr 0.046 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4664 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing