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Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XF0 1XF0.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Potassium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.999597 79.498619
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.008 α = 90 b = 166.008 β = 90 c = 194.942 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2005-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 196.12 98.5 104763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 90
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 1XF0.pdb 2.4 32.73 102788 102788 1972 98.35 0.1672 0.1672 0.16648 0.1701 0.20454 0.167 RANDOM 26.205
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] -0.5 -0.5 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_4_deg 14.307 r_scangle_it 8.761 r_scbond_it 7.698 r_dihedral_angle_1_deg 6.167 r_mcangle_it 4.683 r_mcbond_it 4.372 r_mcbond_other 1.424 r_angle_refined_deg 1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_4_deg 14.307 r_scangle_it 8.761 r_scbond_it 7.698 r_dihedral_angle_1_deg 6.167 r_mcangle_it 4.683 r_mcbond_it 4.372 r_mcbond_other 1.424 r_angle_refined_deg 1.421 r_angle_other_deg 0.961 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_other 0.214 r_nbd_refined 0.19 r_nbd_other 0.188 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.125 r_chiral_restr 0.086 r_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7799 Nucleic Acid Atoms Solvent Atoms 834 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing