4H7C

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with 1-{4-[(2-methyl-1-piperidinyl)sulfonyl]phenyl}-2-pyrrolidinone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION28920% PEG3350, 0.2 M sodium acetate, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3246.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.2α = 90
b = 64.19β = 90
c = 95.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9763DiamondI04

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
11.9753.3499.90.0925.22569425694
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)
11.972.0899.90.354.55.13684

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 REPLACEMENTTHROUGHOUT2FGB1.9753.3413303424338130699.910.164920.162950.2015RANDOM15.754
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]
0.120.61-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.283
r_dihedral_angle_4_deg13.32
r_dihedral_angle_3_deg12.885
r_dihedral_angle_1_deg6.227
r_angle_refined_deg1.957
r_angle_other_deg1.067
r_chiral_restr0.163
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.283
r_dihedral_angle_4_deg13.32
r_dihedral_angle_3_deg12.885
r_dihedral_angle_1_deg6.227
r_angle_refined_deg1.957
r_angle_other_deg1.067
r_chiral_restr0.163
r_bond_refined_d0.02
r_gen_planes_refined0.01
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 Atoms2421
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms70

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling