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NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate
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 7.4 293 0.8% PEG400, 2M Na formate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117 α = 90 b = 54.98 β = 95.74 c = 128.91 γ = 90
Symmetry Space Group P 1 21 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 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8019 EMBL/DESY, HAMBURG X13
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 2.28 16.1 97.9 0.049 73290 44.8
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 MOLREP THROUGHOUT pdb entry 2NAC 2.28 100 73290 69594 3696 97.54 0.1997 0.19596 0.1965 0.2692 0.2673 RANDOM 36.737
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] -3.56 0.01 4.58 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.671 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_1_deg 7.363 r_scangle_it 3.982 r_scbond_it 2.729 r_angle_refined_deg 1.862 r_mcangle_it 1.769 r_mcbond_it 1.052 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.671 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_1_deg 7.363 r_scangle_it 3.982 r_scbond_it 2.729 r_angle_refined_deg 1.862 r_mcangle_it 1.769 r_mcbond_it 1.052 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.305 r_symmetry_hbond_refined 0.242 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.126 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 11504 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement MARHKL data reduction DENZO data reduction SCALEPACK data scaling MOLREP phasing