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Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, 2 -hydroxy-2-hydroxymethyl propanoic 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 3.38 63.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.881 α = 90 b = 112.771 β = 94.7 c = 65.371 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 2016-10-28 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 1.92 37.13 97.7 0.09 0.124 0.085 0.993 7.2 3.8 73981
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 1.92 2.02 97.1 1.194 1.613 1.077 0.31 1.5 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 1.92 37.13 70058 3703 97.19 0.18378 0.18281 0.1942 0.20221 0.2153 RANDOM 41.266
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] -1.28 0.03 1.19 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_4_deg 11.578 r_dihedral_angle_1_deg 5.604 r_long_range_B_refined 4.23 r_long_range_B_other 4.193 r_scangle_other 2.703 r_mcangle_it 2.041 r_mcangle_other 2.04 r_scbond_it 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_4_deg 11.578 r_dihedral_angle_1_deg 5.604 r_long_range_B_refined 4.23 r_long_range_B_other 4.193 r_scangle_other 2.703 r_mcangle_it 2.041 r_mcangle_other 2.04 r_scbond_it 1.69 r_scbond_other 1.689 r_mcbond_it 1.288 r_mcbond_other 1.286 r_angle_refined_deg 1.198 r_angle_other_deg 0.891 r_chiral_restr 0.067 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 5163 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling