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W-formate dehydrogenase V197S from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 26% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.878 α = 90 b = 127.366 β = 90 c = 148.453 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 9M 2023-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.219 48.85 99.7 0.994 7.3 6.1 61458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.219 2.28 0.366
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.219 48.85 61387 3041 99.57 0.221 0.2186 0.2243 0.2638 0.2641 46.356
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] -0.6 -1.062 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.443 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 7.065 r_lrange_other 4.315 r_lrange_it 4.312 r_mcangle_it 2.679 r_mcangle_other 2.679 r_scangle_it 2.224 r_scangle_other 2.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.443 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 7.065 r_lrange_other 4.315 r_lrange_it 4.312 r_mcangle_it 2.679 r_mcangle_other 2.679 r_scangle_it 2.224 r_scangle_other 2.224 r_mcbond_it 1.611 r_mcbond_other 1.611 r_scbond_it 1.302 r_scbond_other 1.302 r_angle_refined_deg 1.262 r_angle_other_deg 1.081 r_nbd_other 0.203 r_nbd_refined 0.178 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.155 r_symmetry_nbd_refined 0.142 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.058 r_symmetry_xyhbond_nbd_refined 0.058 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9235 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing