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W-formate dehydrogenase C872A from Desulfovibrio vulgaris - exposed to oxygen
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 293 22% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.299 α = 90 b = 126.897 β = 90 c = 260.94 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 PILATUS 6M 2020-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979181 ALBA XALOC
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 2.3 148.12 99.5 0.99 8.4 4.5 108727
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 2.3 2.37 0.698
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 6sdr 2.3 48.312 108727 5427 99.779 0.203 0.2004 0.2044 0.2561 0.2576 42.628
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] -2.308 3.506 -1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.174 r_dihedral_angle_4_deg 18.154 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 7.309 r_lrange_it 5.701 r_lrange_other 5.698 r_scangle_it 4.001 r_scangle_other 4.001 r_mcangle_it 3.677 r_mcangle_other 3.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.174 r_dihedral_angle_4_deg 18.154 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 7.309 r_lrange_it 5.701 r_lrange_other 5.698 r_scangle_it 4.001 r_scangle_other 4.001 r_mcangle_it 3.677 r_mcangle_other 3.677 r_scbond_it 2.446 r_scbond_other 2.446 r_mcbond_it 2.369 r_mcbond_other 2.367 r_angle_refined_deg 1.399 r_angle_other_deg 1.152 r_nbd_refined 0.192 r_nbd_other 0.181 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_other 0.079 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.006 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 18540 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 291
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing