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Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.049 α = 90 b = 78.669 β = 90 c = 79.537 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD Beryllium Lenses 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.3 50 99.9 0.052 0.02 0.057 0.023 9.2 5.9 68811 68759 -3 12.1
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 1.3 1.32 100 0.67 0.744 0.318 0.749 2.1 5.4 3380
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XAP 1.3 50 65197 3483 99.9 0.1165 0.1152 0.1401 0.154 RANDOM 15.157
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] 0.06 -0.16 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_sphericity_free 24.475 r_dihedral_angle_4_deg 16.474 r_sphericity_bonded 11.664 r_dihedral_angle_3_deg 11.076 r_dihedral_angle_1_deg 5.461 r_angle_other_deg 1.966 r_mcangle_it 1.705 r_angle_refined_deg 1.46 r_mcbond_it 1.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.524 r_sphericity_free 24.475 r_dihedral_angle_4_deg 16.474 r_sphericity_bonded 11.664 r_dihedral_angle_3_deg 11.076 r_dihedral_angle_1_deg 5.461 r_angle_other_deg 1.966 r_mcangle_it 1.705 r_angle_refined_deg 1.46 r_mcbond_it 1.332 r_mcbond_other 1.332 r_rigid_bond_restr 1.249 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2107 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 48
Software Software Software Name Purpose PDB_EXTRACT data extraction REFMAC refinement HKL-3000 phasing MLPHARE phasing SHELX phasing HKL-3000 data scaling HKL-3000 data reduction BLU-MAX data collection