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W-formate dehydrogenase W491E 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 30% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.824 α = 90 b = 128.043 β = 90 c = 148.748 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 EIGER R 4M 2025-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.993 74.374 93.2 0.9874 7.12 6.98 69547
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 1.993 2.146 0.5072
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 1.993 74.374 69547 3530 81.553 0.211 0.2086 0.217 0.2582 0.2624 35.311
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] 0.137 -0.09 -0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.641 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 12.914 r_lrange_it 7.484 r_lrange_other 7.484 r_dihedral_angle_1_deg 6.521 r_scangle_it 5.69 r_scangle_other 5.689 r_mcangle_it 5.678 r_mcangle_other 5.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.641 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 12.914 r_lrange_it 7.484 r_lrange_other 7.484 r_dihedral_angle_1_deg 6.521 r_scangle_it 5.69 r_scangle_other 5.689 r_mcangle_it 5.678 r_mcangle_other 5.678 r_mcbond_it 4.032 r_mcbond_other 4.031 r_scbond_it 3.964 r_scbond_other 3.963 r_angle_refined_deg 1.225 r_angle_other_deg 1.068 r_nbd_other 0.177 r_nbd_refined 0.172 r_symmetry_nbd_other 0.168 r_symmetry_nbd_refined 0.159 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.045 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 9230 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling