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Crystal structure of human 17-beta-hydroxysteroid dehydrogenase type XI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MR MODEL OBTAINED BY AUTOBUILDING INTO A SELENOMETHIONINE SAD PHASED MAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.08M Sodium Citrate pH5, 2.52M Ammonium Sulphate , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.939 α = 90 b = 110.939 β = 90 c = 118.013 γ = 90
Symmetry Space Group P 41 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 2004-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.95 37 100 0.091 0.091 12.4 61906 61906
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 1.95 2.06 100
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 MR MODEL OBTAINED BY AUTOBUILDING INTO A SELENOMETHIONINE SAD PHASED MAP 1.95 37 52480 52449 1763 99.94 0.16254 0.16254 0.16154 0.1733 0.19212 0.1969 RANDOM 28.395
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] 0.22 0.22 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.691 r_dihedral_angle_4_deg 19.217 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 6.056 r_scangle_it 5.858 r_scbond_it 4.208 r_mcangle_it 2.621 r_mcbond_it 1.765 r_angle_refined_deg 1.344 r_angle_other_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.691 r_dihedral_angle_4_deg 19.217 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 6.056 r_scangle_it 5.858 r_scbond_it 4.208 r_mcangle_it 2.621 r_mcbond_it 1.765 r_angle_refined_deg 1.344 r_angle_other_deg 0.792 r_mcbond_other 0.42 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.204 r_symmetry_vdw_other 0.201 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.161 r_nbd_other 0.158 r_chiral_restr 0.083 r_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3651 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing