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NAD-dependent formate dehydrogenase from Pseudomonas sp.101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAC PDB ENTRY 2NAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 290 Ammonium Sulfate (48% saturated), 8% MPD, 0.1M HEPES, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.54 51.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.3 α = 90 b = 93.3 β = 90 c = 103.05 γ = 90
Symmetry Space Group P 42 21 2
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 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 1.009 EMBL/DESY, HAMBURG X11
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 2.1 69.01 94.7 0.078 31389 29590
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 2.1 2.13 91.3 0.495
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2NAC 2.1 69.01 27157 24447 1319 94.71 0.209 0.18923 0.18625 0.1866 0.24224 0.2433 RANDOM 30.754
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] 1.46 1.46 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.997 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 15.812 r_dihedral_angle_1_deg 7.148 r_scangle_it 4.09 r_scbond_it 2.744 r_angle_refined_deg 1.737 r_mcangle_it 1.694 r_mcbond_it 1.034 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.997 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 15.812 r_dihedral_angle_1_deg 7.148 r_scangle_it 4.09 r_scbond_it 2.744 r_angle_refined_deg 1.737 r_mcangle_it 1.694 r_mcbond_it 1.034 r_nbtor_refined 0.313 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2920 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MARHKL data reduction DENZO data reduction SCALEPACK data scaling MOLREP phasing