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Corynebacterium glutamicum pyruvate:quinone oxidoreductase (PQO) purified from bacteria grown in acetate minimal medium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 22 % (w/v) PEG 4000, 0.2 M (NH4)2SO4, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.044 α = 90 b = 119.072 β = 90 c = 155.305 γ = 90
Symmetry Space Group I 2 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 EIGER2 X CdTe 16M 2021-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.219 77.652 94.1 0.1206 0.1259 0.0358 0.997 10.77 12.16 144969
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) 1.219 1.322 59.7 2.1217 2.2102 0.6157 0.694 1.67 12.64 7248
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3EYA 1.219 17.67 144896 7182 77.6 0.1766 0.1757 0.1657 0.1922 0.1807 RANDOM 19.78
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] 0.444 -0.2704 -0.1736
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.9 t_other_torsion 2.56 t_angle_deg 1.2 t_bond_d 0.013 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4323 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 80
Software Software Software Name Purpose BUSTER refinement autoPROC data processing autoPROC data processing Aimless data scaling autoPROC data reduction PHASER phasing