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Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PEG 3350, Tacsimate (Hampton Research, USA)
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.794 α = 90 b = 95.789 β = 99.282 c = 117.93 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2021-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 97.9 0.08 24.6 3.4 143534
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.287
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 THROUGHOUT 4XYB 1.8 34.138 140486 7007 97.707 0.157 0.1552 0.1554 0.1908 0.1908 17.076
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] 0.855 -1.96 1.168 -1.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.154 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_2_deg 10.777 r_dihedral_angle_1_deg 7.136 r_lrange_it 4.207 r_lrange_other 4.17 r_scangle_it 3.502 r_scangle_other 3.502 r_scbond_it 2.247 r_scbond_other 2.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.154 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_2_deg 10.777 r_dihedral_angle_1_deg 7.136 r_lrange_it 4.207 r_lrange_other 4.17 r_scangle_it 3.502 r_scangle_other 3.502 r_scbond_it 2.247 r_scbond_other 2.247 r_mcangle_it 1.826 r_mcangle_other 1.826 r_angle_refined_deg 1.533 r_mcbond_it 1.346 r_mcbond_other 1.338 r_angle_other_deg 0.527 r_nbd_refined 0.219 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.176 r_nbd_other 0.168 r_symmetry_nbd_refined 0.155 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11796 Nucleic Acid Atoms Solvent Atoms 965 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing