1ZQ5

Crystal structure of human androgenic 17beta-hydroxysteroid dehydrogenase type 5 in complexed with a potent inhibitor EM1404


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XF0PDB ENTRY 1XF0

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.347α = 90
b = 62.781β = 90
c = 95.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C0.9795NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.329.8495.68287875293

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 1XF01.329.848287875293394795.610.181740.181740.180890.19731RANDOM12.757
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.972
r_dihedral_angle_4_deg16.888
r_dihedral_angle_3_deg12.638
r_dihedral_angle_1_deg5.3
r_scangle_it1.748
r_angle_refined_deg1.332
r_scbond_it1.239
r_mcangle_it0.953
r_mcbond_it0.58
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.972
r_dihedral_angle_4_deg16.888
r_dihedral_angle_3_deg12.638
r_dihedral_angle_1_deg5.3
r_scangle_it1.748
r_angle_refined_deg1.332
r_scbond_it1.239
r_mcangle_it0.953
r_mcbond_it0.58
r_nbtor_refined0.318
r_nbd_refined0.22
r_symmetry_vdw_refined0.131
r_xyhbond_nbd_refined0.115
r_chiral_restr0.092
r_symmetry_hbond_refined0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2719
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms81

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling