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Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5.6 277 PEG-4000 22%, 0.1M NaCitrate, pH 5.6, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.788 α = 90 b = 144.788 β = 90 c = 203.885 γ = 120
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 MAR CCD 130 mm 2005-12-03 M SINGLE WAVELENGTH 2 1 x-ray M 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 1.000 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 19.98 99.7 0.068 0.066 18.29 7.4 75962 75736 29.947
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.8 1.9 97.6 0.278 0.458 4.4 7.4 11281
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HDJ 1.8 19.98 74951 3811 99.7 0.204 0.2029 0.228 0.2258 RANDOM 28.6
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] 1.65 1.49 1.65 -3.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 2.31 c_mcangle_it 1.73 c_scbond_it 1.69 c_angle_deg 1.3 c_mcbond_it 1.16 c_improper_angle_d 0.86 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 193
Software Software Software Name Purpose XSCALE data processing CNS refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction XSCALE data scaling