2O23

The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U7Tpdb entry 1U7T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729325.5% PEG 3350, 15% glycerol, 0.17 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.037α = 90
b = 117.037β = 90
c = 69.087γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.25099.50.0928.13.616858516858511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2699.21.92.924386

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1U7T1.250166548166548199699.490.1230.1230.122640.15395RANDOM11.171
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]
-0.45-0.22-0.450.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_sphericity_free20.149
r_dihedral_angle_4_deg16.141
r_dihedral_angle_3_deg11.222
r_scangle_it8.854
r_scbond_it7.416
r_sphericity_bonded7.413
r_dihedral_angle_1_deg5.857
r_mcangle_it5.149
r_mcbond_it4.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_sphericity_free20.149
r_dihedral_angle_4_deg16.141
r_dihedral_angle_3_deg11.222
r_scangle_it8.854
r_scbond_it7.416
r_sphericity_bonded7.413
r_dihedral_angle_1_deg5.857
r_mcangle_it5.149
r_mcbond_it4.51
r_rigid_bond_restr3.737
r_mcbond_other2.796
r_angle_refined_deg1.55
r_angle_other_deg0.961
r_symmetry_vdw_refined0.257
r_nbd_refined0.224
r_symmetry_vdw_other0.215
r_nbd_other0.194
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.142
r_chiral_restr0.091
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3582
Nucleic Acid Atoms
Solvent Atoms614
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing