3WIO

Crystal structure of OSD14 in complex with hydroxy D-ring


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52778% PEG 20000, 2% 1,4-DIOXANE, 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1141.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.38α = 90
b = 88.13β = 90
c = 119.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77IMAGE PLATERIGAKU RAXIS VII2012-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1200.08620.47.130394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.150.435.27

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 REPLACEMENTTHROUGHOUT3VXK2.1202885815371000.1910.1880.246RANDOM22.01
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]
0.49-0.540.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.963
r_dihedral_angle_4_deg20.751
r_dihedral_angle_3_deg17.731
r_dihedral_angle_1_deg6.307
r_scangle_it4.764
r_scbond_it3.13
r_angle_refined_deg1.879
r_mcangle_it1.865
r_mcbond_it1.05
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.963
r_dihedral_angle_4_deg20.751
r_dihedral_angle_3_deg17.731
r_dihedral_angle_1_deg6.307
r_scangle_it4.764
r_scbond_it3.13
r_angle_refined_deg1.879
r_mcangle_it1.865
r_mcbond_it1.05
r_chiral_restr0.128
r_bond_refined_d0.022
r_gen_planes_refined0.009
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_other
r_long_range_B_refined
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 Atoms4108
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms8

Software

Software
Software NamePurpose
Crystaldata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling