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W-formate dehydrogenase C872A from Desulfovibrio vulgaris - with Formamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 34% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.467 α = 73.868 b = 74.949 β = 89.135 c = 122.806 γ = 71.123
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 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 ESRF ID23-1
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 1.416 117.57 92.3 0.997 8.01 2 346803
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 1.416 1.54 0.658
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.416 117.57 346803 17188 75.752 0.15 0.1485 0.1757 0.1848 18.1
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] 0.066 -0.058 0.01 -0.059 -0.016 -0.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.006 r_dihedral_angle_1_deg 6.927 r_lrange_it 4.461 r_lrange_other 4.461 r_scangle_it 3.608 r_scangle_other 3.608 r_scbond_it 2.403 r_scbond_other 2.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.006 r_dihedral_angle_1_deg 6.927 r_lrange_it 4.461 r_lrange_other 4.461 r_scangle_it 3.608 r_scangle_other 3.608 r_scbond_it 2.403 r_scbond_other 2.403 r_mcangle_it 1.977 r_mcangle_other 1.977 r_angle_refined_deg 1.696 r_angle_other_deg 1.475 r_mcbond_it 1.398 r_mcbond_other 1.398 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.213 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.174 r_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.109 r_chiral_restr 0.097 r_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18544 Nucleic Acid Atoms Solvent Atoms 1718 Heterogen Atoms 438
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