☰ Navigation Tabs
Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, L-tartaric acid 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 3.44 64.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.622 α = 90 b = 113.109 β = 94.61 c = 65.82 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 2016-10-19 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 2.65 29.6 99.4 0.099 0.137 0.094 0.994 5.5 3.8 29362
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 2.65 2.79 99.9 0.827 1.134 0.772 0.538 1.1 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5UHW 2.65 26.6 27812 1468 99.34 0.20594 0.20424 0.211 0.23881 0.248 RANDOM 56.159
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] -0.81 -0.11 -0.71 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_dihedral_angle_4_deg 14.789 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 2.517 r_long_range_B_other 2.517 r_angle_refined_deg 1.268 r_mcangle_it 1.257 r_mcangle_other 1.257 r_scangle_other 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_dihedral_angle_4_deg 14.789 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 2.517 r_long_range_B_other 2.517 r_angle_refined_deg 1.268 r_mcangle_it 1.257 r_mcangle_other 1.257 r_scangle_other 1.08 r_angle_other_deg 0.9 r_mcbond_it 0.712 r_mcbond_other 0.712 r_scbond_it 0.607 r_scbond_other 0.606 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 5185 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 110
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement