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Crystal structure of aldose reductase A1-R complexed with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFM PDB ENTRY 3AFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 47% 2-methyl-2,4-pentanediol, 2% tert-butanol, 0.5mM NADP, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.404 α = 80.15 b = 64.195 β = 66.08 c = 74.441 γ = 64.98
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 RIGAKU JUPITER 210 2008-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 1.63 50 95.9 0.035 19.7 2.6 115155
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) 1.63 1.69 88.8 0.179 3.82 2.4
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 PDB ENTRY 3AFM 1.63 22.68 104849 5537 95.87 0.17411 0.1723 0.1718 0.20858 0.2075 RANDOM 19.711
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_dihedral_angle_2_deg 37.08 r_dihedral_angle_4_deg 11.752 r_dihedral_angle_3_deg 10.901 r_dihedral_angle_1_deg 4.929 r_scangle_it 1.653 r_scbond_it 1.092 r_angle_refined_deg 1.056 r_mcangle_it 0.77 r_mcbond_it 0.449 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.08 r_dihedral_angle_4_deg 11.752 r_dihedral_angle_3_deg 10.901 r_dihedral_angle_1_deg 4.929 r_scangle_it 1.653 r_scbond_it 1.092 r_angle_refined_deg 1.056 r_mcangle_it 0.77 r_mcbond_it 0.449 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.101 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7568 Nucleic Acid Atoms Solvent Atoms 927 Heterogen Atoms 212
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling