4FA3

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (R)-1-(naphthalen-2-ylsulfonyl)piperidine-3-carboxylic acid (86)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FGB 

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
2.346.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.127α = 90
b = 63.469β = 90
c = 96.445γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+Varimax HF Optics2010-03-31MSINGLE 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
12.218.6897.60.0962.91791517915
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)
12.22.2893.50.3421.92.41656

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 REPLACEMENTTHROUGHOUT2FGB2.218.68515791700091597.430.211150.207720.27808RANDOM23.701
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]
-1.08-0.631.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.901
r_dihedral_angle_3_deg15.748
r_dihedral_angle_4_deg14.28
r_dihedral_angle_1_deg6.793
r_scangle_it3.724
r_scbond_it2.571
r_angle_refined_deg1.848
r_mcangle_it1.578
r_angle_other_deg1.045
r_mcbond_it0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.901
r_dihedral_angle_3_deg15.748
r_dihedral_angle_4_deg14.28
r_dihedral_angle_1_deg6.793
r_scangle_it3.724
r_scbond_it2.571
r_angle_refined_deg1.848
r_mcangle_it1.578
r_angle_other_deg1.045
r_mcbond_it0.906
r_mcbond_other0.261
r_chiral_restr0.12
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2414
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms78

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement