☰ Navigation Tabs
Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VMD PDB entry 1vmd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Rigaku Reagents JCSG+ screen, condition a11: 50% (V/V) MPD, 200mM ammonium phosphate monobasic, Tris base / HCl pH 8.5. ElanA.00692.a.B1.PS38386 at 18.2mg/ml: cryo: direct: tray: 2978372 a11: puck vsf3-5
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.59 α = 90 b = 167.59 β = 90 c = 159.9 γ = 90
Symmetry Space Group P 43 21 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 CCD RAYONIX MX-300 2018-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.1 48.61 99.9 0.101 0.107 0.999 19.3 9.996 132174 29.637
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 0.559 0.588 0.928 4.5 10.042
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1vmd 2.1 48.61 1.34 132058 2162 99.88 0.1481 0.1475 0.1484 0.1841 0.1833 0 28.5545
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 14.822 f_angle_d 0.873 f_chiral_restr 0.06 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14161 Nucleic Acid Atoms Solvent Atoms 1238 Heterogen Atoms 76
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing PHASER phasing Coot model building