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NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution (2ml): 14 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA, 5mM sodium azide, 5mM NAD. Reservoir solution (2ml): 0.1M Bis-Tris, pH 5.5, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.71 66.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.62 α = 90 b = 217.68 β = 92.62 c = 139.11 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.99 KURCHATOV SNC K4.4
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 2 19.99 93.6 0.075 8.93 2.1 457766 428654 25.095
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) 2 2.07 87.9 0.328 2.6 1.8 39349
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2 19.99 434297 421051 22264 96.95 0.191 0.189 0.1909 0.231 0.2317 RANDOM 24.463
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] 0.61 -1.28 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.014 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.457 r_scangle_it 3.742 r_scbond_it 2.415 r_angle_refined_deg 1.639 r_mcangle_it 1.419 r_mcbond_it 0.807 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.014 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.457 r_scangle_it 3.742 r_scbond_it 2.415 r_angle_refined_deg 1.639 r_mcangle_it 1.419 r_mcbond_it 0.807 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32868 Nucleic Acid Atoms Solvent Atoms 3745 Heterogen Atoms 723
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction AUTOMAR data collection XDS data reduction