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Crystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a ternary complex with NADPH and glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M SPG
25% PEG 1500
In-drop protein concentration of 13 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.2328458 44.947571
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.853 α = 90 b = 82.853 β = 90 c = 77.255 γ = 120
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-F 2019-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.5 52.57 100 0.082 0.086 0.025 0.999 14.7 11.9 48238
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 1.5 1.53 99.9 1.67 1.77 0.582 0.746 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BBY 1.5 52.51 45844 2368 99.96 0.1672 0.1658 0.1794 0.1945 0.2101 RANDOM 21.006
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] -1.19 -0.59 -1.19 3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.731 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 11.707 r_dihedral_angle_1_deg 6.082 r_angle_refined_deg 1.725 r_angle_other_deg 1.532 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.731 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 11.707 r_dihedral_angle_1_deg 6.082 r_angle_refined_deg 1.725 r_angle_other_deg 1.532 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2178 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing