4XVE

17beta-HSD5 in complex with 3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S1P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52980.1 M sodium citrate, 0.4 M ammonium acetate, 2.5% (v/v) 2-methyl-2,4-pentanediol, 22-30% (w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1843.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.269α = 90
b = 62.554β = 90
c = 95.655γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 2102005-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.555099.48.13.546111
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)
1.551.6197.40.4542.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S1P1.5541.4246111246399.40.180390.179120.20308RANDOM14.869
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]
-0.020.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.785
r_dihedral_angle_4_deg18.391
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg6.233
r_long_range_B_refined5.746
r_scbond_it3.036
r_mcangle_it2.752
r_angle_refined_deg2.575
r_mcbond_it1.795
r_chiral_restr0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.785
r_dihedral_angle_4_deg18.391
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg6.233
r_long_range_B_refined5.746
r_scbond_it3.036
r_mcangle_it2.752
r_angle_refined_deg2.575
r_mcbond_it1.795
r_chiral_restr0.181
r_bond_refined_d0.026
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2524
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing