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Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and glycerol. Resolution: 1.79 A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.826 α = 90 b = 109.833 β = 90 c = 129.186 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 225 mm CCD Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror. 2007-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 1.79 50 98.6 0.109 20.5 4.1 66774 66774
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 1.79 1.85 100 0.37 3.4 4.1 6684
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS 3BUR 1.79 50 63320 63320 2800 0.2361 0.2361 0.1931 0.2571 0.1966 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 s_non_zero_chiral_vol 0.031 s_from_restr_planes 0.024 s_bond_d 0.02 s_angle_d 0.012 s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5254 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 114
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing