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Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES, 25% PEG 3000, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.931 α = 90 b = 116.617 β = 106.9 c = 63.208 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 NOIR-1 2013-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 41.98 95.5 0.051 14.8 3.1 107639
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 1.5 1.58 88.5 0.331 3.4 2.9
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 FREE R-VALUE 2J6I 1.5 41.976 0.19 107560 10639 95.48 0.1398 0.1383 0.1365 0.1691 0.1663
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 13.159 f_angle_d 1.288 f_chiral_restr 0.073 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5636 Nucleic Acid Atoms Solvent Atoms 1084 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data scaling Coot model building PHASER phasing Blu-Ice data collection SCALA data scaling