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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Same Batch SSX 2025/04/01
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 26% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.27 45.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.898 α = 90 b = 127.884 β = 90 c = 149.398 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 X CdTe 16M 2025-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.953 59.524 98.84 0.9993 18.801 13.11 89865 29.18
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 1.953 1.987 0.739
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 1.953 59.524 89865 4482 98.793 0.214 0.2122 0.2171 0.251 0.2533 39.827
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] 0.788 -0.769 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.559 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_1_deg 6.649 r_lrange_it 3.714 r_lrange_other 3.671 r_mcangle_it 2.075 r_mcangle_other 2.075 r_scangle_it 1.725 r_scangle_other 1.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.559 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_1_deg 6.649 r_lrange_it 3.714 r_lrange_other 3.671 r_mcangle_it 2.075 r_mcangle_other 2.075 r_scangle_it 1.725 r_scangle_other 1.725 r_mcbond_it 1.219 r_mcbond_other 1.219 r_angle_refined_deg 1.212 r_angle_other_deg 1.087 r_scbond_it 1.004 r_scbond_other 1.004 r_nbd_other 0.183 r_nbd_refined 0.174 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.155 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.053 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_refined 0.043 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 9234 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement autoPROC data processing PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling