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Apo-form of NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C-1 in closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSD PDB ENTRY 2GSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein solution (2mcl): 10.5 mg/ml FDH, 0.1M Na2HPO4 pH 7.0, Reservoir solution (2mcl): 0.1M HEPES pH 7.5, 2.2M Ammonium Sulfate, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.66 α = 90 b = 66.089 β = 104.13 c = 75.551 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 2006-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 1.05 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 1.96 39.1 99.5 0.122 2.4 3.3 27787 27648 33.1
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 1.96 2.05 100 0.476 1.3 3.3 3430
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2GSD 1.96 39.1 27787 27648 1393 99.53 0.19 0.187 0.1919 0.24 0.2491 RANDOM 32.438
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] 0.24 -0.83 0.34 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.767 r_dihedral_angle_3_deg 14.097 r_dihedral_angle_4_deg 13.427 r_dihedral_angle_1_deg 6.883 r_scangle_it 3.993 r_scbond_it 2.687 r_angle_refined_deg 1.82 r_mcangle_it 1.702 r_mcbond_it 1.015 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.767 r_dihedral_angle_3_deg 14.097 r_dihedral_angle_4_deg 13.427 r_dihedral_angle_1_deg 6.883 r_scangle_it 3.993 r_scbond_it 2.687 r_angle_refined_deg 1.82 r_mcangle_it 1.702 r_mcbond_it 1.015 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2996 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 11
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction AUTOMAR data collection AUTOMAR data reduction