1XJB

Crystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with NADP(H), citrate and acetate molecules


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.7293Sodium citrate, PEG4000, Lithium sulfate, pH 5.7, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.12α = 90
b = 143.12β = 90
c = 204.31γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IImonochromator2001-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.919.170.0850.06317.84.759186568661
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9288.90.3750.4663.44.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1J961.919.17568665686630031000.174860.173610.19855RANDOM32.498
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_deg37.022
r_dihedral_angle_4_deg15.872
r_dihedral_angle_3_deg11.878
r_dihedral_angle_1_deg9.25
r_scangle_it4.459
r_scbond_it3.523
r_mcangle_it2.152
r_angle_refined_deg2.027
r_mcbond_it1.711
r_nbd_refined0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.022
r_dihedral_angle_4_deg15.872
r_dihedral_angle_3_deg11.878
r_dihedral_angle_1_deg9.25
r_scangle_it4.459
r_scbond_it3.523
r_mcangle_it2.152
r_angle_refined_deg2.027
r_mcbond_it1.711
r_nbd_refined0.236
r_symmetry_vdw_refined0.23
r_xyhbond_nbd_refined0.162
r_chiral_restr0.151
r_symmetry_hbond_refined0.135
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms5183
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
AMoREphasing
CNSrefinement
Crystaldata collection
CrystalCleardata reduction
XDSdata scaling