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Crystal structure of Escherichia coli Glyoxalase II with L-Tartrate in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.02M Sodium formate, 0.02M Ammonium acetate, 0.02M Sodium citrate tribasic dihydrate, 0.02M Sodium potassium tartrate tetrahydrate, 0.02M Sodium oxamate; 0.1 M sodium HEPES and MOPS (acid), pH 7.5; 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.053 α = 90 b = 43.655 β = 90 c = 159.067 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 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.8 29.4 99 0.103 0.107 0.031 0.999 16.4 11.6 25769
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 1.8 1.85 89.7 0.693 0.75 0.277 0.786 6.7
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 6RZ0 1.803 29.398 1.36 25700 2000 98.96 0.164 0.1614 0.1623 0.1969 0.1979 29.8172
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 1931 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction