☰ Navigation Tabs
Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, D-Apionate and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5 M Sodium formate, 5 mM NAD+, 5 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.48 64.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.763 α = 90 b = 114.183 β = 94.99 c = 66.158 γ = 90
Symmetry Space Group C 1 2 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 315 Diamond 2016-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 29.57 98.2 0.042 0.058 0.039 0.999 6.6 3.8 51035
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 98 0.659 0.891 0.596 0.795 1.4 3.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5UHW 2.2 29.57 47565 2486 96.32 0.20126 0.19996 0.2259 0.2529 RANDOM 63.078
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] -2.49 1.77 1.64 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_3_deg 12.776 r_dihedral_angle_4_deg 12.139 r_dihedral_angle_1_deg 5.544 r_long_range_B_refined 4.988 r_long_range_B_other 4.98 r_scangle_other 2.934 r_mcangle_it 2.504 r_mcangle_other 2.504 r_scbond_it 1.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_3_deg 12.776 r_dihedral_angle_4_deg 12.139 r_dihedral_angle_1_deg 5.544 r_long_range_B_refined 4.988 r_long_range_B_other 4.98 r_scangle_other 2.934 r_mcangle_it 2.504 r_mcangle_other 2.504 r_scbond_it 1.843 r_scbond_other 1.84 r_mcbond_it 1.564 r_mcbond_other 1.564 r_angle_refined_deg 1.23 r_angle_other_deg 0.883 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5158 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling