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Aflatoxin aldehyde reductase (AKR7A1) from Rat Liver
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EXB PDB ENTRY 1EXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 SITTING DROP METHOD WITH 1MICROLITRE PROTEIN (6 MG/ML) AND 1MICROLITRE WELL 20% PEG8K, 0.2M LITHIUM SULPHATE, 0.1M SODIUM CITRATE PH 5.
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.54 α = 90 b = 64.68 β = 91.03 c = 112.84 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 IMAGE PLATE MAR scanner 345 mm plate BENT MIRROR 2000-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.38 30 85.4 0.046 24 2.8 134602
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 1.38 1.43 43 0.467 1.2 2.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EXB 1.38 28.75 3768 7094 73.7 0.159 0.158 0.18 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.577 r_scbond_it 3.338 r_dihedral_angle_3_deg 2.207 r_mcangle_it 2.143 r_angle_other_deg 1.701 r_mcbond_it 1.589 r_symmetry_hbond_refined 0.579 r_nbtor_other 0.296 r_nbd_refined 0.243 r_nbd_other 0.205
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.577 r_scbond_it 3.338 r_dihedral_angle_3_deg 2.207 r_mcangle_it 2.143 r_angle_other_deg 1.701 r_mcbond_it 1.589 r_symmetry_hbond_refined 0.579 r_nbtor_other 0.296 r_nbd_refined 0.243 r_nbd_other 0.205 r_symmetry_vdw_other 0.195 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.107 r_xyhbond_nbd_other 0.042 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4895 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing