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quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 288.15 reservoir:
25% w/v pentaerythriol propoxylate (17/8 PO/OH),
100 mM Tris pH 8.5,
50 mM Magnesium chloride
condition:
10% w/v pentaerythriol propoxylate (17/8 PO/OH),
40 mM Tris pH 8.5,
30 mM Magnesium chloride,
4 mg/mL Protein,
10 mM HEPES-KOH pH 7.8,
30 mM NaCl,
2 mM TPP,
1 mM CoA
Crystal Properties Matthews coefficient Solvent content 3.17 61.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.094 α = 90 b = 180.337 β = 90 c = 202.008 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 2020-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 29.941 99.8 0.266 0.277 0.074 0.997 10.1 13.6 144506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99.4 0.829 0.829 0.86 0.227 0.976 0.8 14
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 7AYG 2.8 29.94 0.76 143868 1996 99.48 0.2022 0.2018 0.2315 0.2135 29.3
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 21.9271 f_angle_d 0.5593 f_chiral_restr 0.0452 f_plane_restr 0.0039 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32512 Nucleic Acid Atoms Solvent Atoms 1272 Heterogen Atoms 432
Software Software Software Name Purpose PHENIX refinement XDS data reduction pointless data scaling PHASER phasing