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W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.18 α = 90 b = 127.926 β = 90 c = 149.467 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 PILATUS3 6M 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9686 ESRF ID30B
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 2.06 97.19 87.87 0.991 7 4.3 65092
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 2.06 2.15 0.495
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6SDV 2.06 97.19 65087 3244 82.903 0.209 0.2064 0.2162 0.2549 0.2629 40.723
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] 0.21 -0.119 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.648 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 14.396 r_dihedral_angle_1_deg 7.287 r_lrange_it 6.163 r_lrange_other 6.156 r_mcangle_it 4.565 r_mcangle_other 4.565 r_scangle_it 4.373 r_scangle_other 4.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.648 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 14.396 r_dihedral_angle_1_deg 7.287 r_lrange_it 6.163 r_lrange_other 6.156 r_mcangle_it 4.565 r_mcangle_other 4.565 r_scangle_it 4.373 r_scangle_other 4.372 r_mcbond_other 3.099 r_mcbond_it 3.098 r_scbond_it 2.898 r_scbond_other 2.888 r_angle_refined_deg 1.393 r_angle_other_deg 1.153 r_symmetry_xyhbond_nbd_refined 0.301 r_nbd_refined 0.194 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.16 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.104 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 207 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