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NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C2 in complex with NAD and azide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M Bis-Tris, 1.8M Ammonium Sulfate, 5mM NAD, 5mM azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.45 α = 90 b = 66.5 β = 103.57 c = 75.55 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 293 IMAGE PLATE MAR scanner 345 mm plate 2006-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-6 1.5418
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 1.95 73.52 99.3 0.095 65949 28153 26.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.03 88
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 (All) 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 MOLREP THROUGHOUT 2NAD 1.95 73.52 65949 26730 1422 99.22 0.159 0.14441 0.14231 0.1432 0.18385 0.1847 RANDOM 18.954
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] 0.23 -0.57 0.14 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.619 r_dihedral_angle_4_deg 15.975 r_dihedral_angle_3_deg 14.032 r_dihedral_angle_1_deg 6.422 r_scangle_it 3.912 r_scbond_it 2.552 r_mcangle_it 1.659 r_angle_refined_deg 1.619 r_mcbond_it 1.06 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.619 r_dihedral_angle_4_deg 15.975 r_dihedral_angle_3_deg 14.032 r_dihedral_angle_1_deg 6.422 r_scangle_it 3.912 r_scbond_it 2.552 r_mcangle_it 1.659 r_angle_refined_deg 1.619 r_mcbond_it 1.06 r_nbtor_refined 0.301 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3084 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction XSCALE data scaling MOLREP phasing