4HMN

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (4-(4-Chlorophenyl)piperazin-1-yl)(morpholino)methanone (24)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28920% PEG3350, 0.2 M sodium acetate , VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3647.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.956α = 90
b = 64.068β = 90
c = 96.404γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+Varimax HF Optics2010-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54182

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
12.418.5397.60.0681419114191
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4990.70.2462.82.51277

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FGB2.418.53134881348870297.360.22230.218660.29656RANDOM26.034
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]
0.66-0.11-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.168
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg12.749
r_dihedral_angle_1_deg6.742
r_angle_refined_deg1.78
r_angle_other_deg0.991
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.168
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg12.749
r_dihedral_angle_1_deg6.742
r_angle_refined_deg1.78
r_angle_other_deg0.991
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2437
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms73

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement