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Crystal structure of human Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and HEPES. Resolution: 1.35 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 10-20% wt/vol Peg 4000; 10% isopropanol; 100mM Hepes pH 7.5; 2.0 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.711 α = 90 b = 109.798 β = 90 c = 128.023 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 2007-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.00 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 1.35 50 95.7 0.094 22.6 147700 147700 14.6
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 1.35 1.4 89.6 0.411 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.35 33.69 140579 140579 7075 91 0.218 0.218 0.2154 0.232 0.2172 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] -3.28 -4.79 8.06
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.59 c_scbond_it 1.76 c_mcangle_it 1.59 c_angle_deg 1.2 c_mcbond_it 1.03 c_improper_angle_d 0.87 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.59 c_scbond_it 1.76 c_mcangle_it 1.59 c_angle_deg 1.2 c_mcbond_it 1.03 c_improper_angle_d 0.87 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5254 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 123
Software Software Software Name Purpose ADSC data collection CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing