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PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000090873
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 100 mM TRIS, 25% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.472 α = 90 b = 101.247 β = 90 c = 144.384 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11581 ALS 8.3.1
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 1.99 48.13 100 0.128 0.139 0.054 0.998 10.1 6.5 44628 39.16
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 1.99 2.04 99.8 2.557 2.793 1.109 0.307 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.99 47.77 1.35 44460 2210 99.72 0.2337 0.2308 0.2307 0.2866 0.2863 57.9963
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4821 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing