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Crystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 MCSG1 D10 (269027d10): 0.2 M Calcium Acetate 0.1 M Sodium Cacodylate:HCl pH 6.5 40% (v/v ) PEG 300; protein conc. 20.9mg/mL; 5mM NADP soak; direct cryo; puck foe9-7
Crystal Properties Matthews coefficient Solvent content 2.03 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.81 α = 90 b = 49.23 β = 94.99 c = 66.96 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN 944+ RIGAKU VARIMAX 2016-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 99 0.11 0.993 8.59 3.23 27131 -3 15.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 97.1 0.346 2.63 2.13
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 5IDQ 2 50 1.35 27115 1703 98.98 0.1849 0.1813 0.237 0.2111 20.1734
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 14.965 f_angle_d 0.825 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3297 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 96
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction Coot model building XDS data reduction