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Crystal structure of formate dehydrogenase FDH2 D222S/Q223R enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP and azide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.005 M Cobalt(II) chloride hexahydrate,
0.005 M Cadmium chloride hemi(pentahydrate),
0.005 M Magnesium chloride hexahydrate,
0.005 M Nickel(II) chloride hexahydrate,
0.1 M HEPES pH 7.5,
12 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.903 α = 90 b = 60.783 β = 90 c = 131.682 γ = 90
Symmetry Space Group P 2 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 S 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 1.00 ESRF MASSIF-3
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 1.97 45.67 99.87 0.077 16.7 7.3 28252 207048 17.91
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 1.97 2.04 0.259 6.3 7.46 30645
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 THROUGHOUT 6T8C 1.98 35.585 1.34 52681 2581 99.73 0.1563 0.1537 0.1718 0.2064 0.2129 24.9831
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2911 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing