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Crystal structure of human liver delta(4)-3-ketosteroid 5beta-reductase (akr1d1) in complex with progesterone and nadp. Resolution: 2.03 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 isopropanol 10%,peg 4000, tris-HCl 100 mM pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.743 α = 90 b = 109.434 β = 90 c = 128.583 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 ADSC QUANTUM 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2008-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.008 NSLS X29A
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 2.03 50 97.6 0.131 12.2 45518 44101
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) 2.03 2.15 96.9 0.58 2 4301
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 FOURIER SYNTHESIS THROUGHOUT 3bur 2.03 25.04 41289 1866 90.7 0.194 0.194 0.1978 0.234 0.1995 RANDOM 27.9
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] -1.11 -8.56 9.67
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.95 c_scbond_it 2.06 c_mcangle_it 2 c_mcbond_it 1.29 c_angle_deg 1.1 c_improper_angle_d 0.86 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5254 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 142
Software Software Software Name Purpose CNS refinement CBASS data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing