7X3Z

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NAD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP300KH2PO4, PEG 8000
Crystal Properties
Matthews coefficientSolvent content
1.9536.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.05α = 90
b = 108.15β = 90
c = 117.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2018-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.252599.90.2020.0750.9837.97.326759
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.252.371000.5090.1850.9327.4

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 REPLACEMENTTHROUGHOUT1JTV2.2524.9925322138299.830.193160.189820.25465RANDOM39.441
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]
2.35-3.811.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.04
r_dihedral_angle_2_deg9.548
r_long_range_B_refined8.68
r_long_range_B_other8.679
r_dihedral_angle_1_deg7.68
r_scangle_other6.661
r_mcangle_other5.163
r_mcangle_it5.162
r_scbond_it4.417
r_scbond_other4.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.04
r_dihedral_angle_2_deg9.548
r_long_range_B_refined8.68
r_long_range_B_other8.679
r_dihedral_angle_1_deg7.68
r_scangle_other6.661
r_mcangle_other5.163
r_mcangle_it5.162
r_scbond_it4.417
r_scbond_other4.416
r_mcbond_it3.546
r_mcbond_other3.546
r_angle_refined_deg1.606
r_angle_other_deg0.507
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4248
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction