3O4R

Crystal Structure of Human Dehydrogenase/Reductase (SDR family) member 4 (DHRS4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZATPDB ENTRY 2ZAT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172770.1M KSCN30% mPEG 2K, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.07α = 90
b = 132.2β = 90
c = 133.796γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR2252010-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.729.2999.10.070.0710.44.8116449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7999.91.74.9

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 2ZAT1.729.29110448110448582998.60.2120.210.25RANDOM25.85
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]
-3.84.56-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.546
r_dihedral_angle_4_deg20.308
r_dihedral_angle_3_deg12.247
r_dihedral_angle_1_deg5.549
r_scangle_it5.114
r_scbond_it3.554
r_mcangle_it2.838
r_mcbond_it1.918
r_angle_refined_deg1.372
r_mcbond_other0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.546
r_dihedral_angle_4_deg20.308
r_dihedral_angle_3_deg12.247
r_dihedral_angle_1_deg5.549
r_scangle_it5.114
r_scbond_it3.554
r_mcangle_it2.838
r_mcbond_it1.918
r_angle_refined_deg1.372
r_mcbond_other0.931
r_angle_other_deg0.906
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7416
Nucleic Acid Atoms
Solvent Atoms606
Heterogen Atoms235

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling