3VXK

Crystal structure of OsD14


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52938% PEG 20000, 2% 1,4-dioxane, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.14α = 90
b = 88.72β = 90
c = 118.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 2702011-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
11.75200.076227.151922
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)
11.751.80.3376.55.5

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 REPLACEMENTTHROUGHOUT1WOM1.752049279264399.920.182830.18070.22261RANDOM13.061
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]
0.39-0.520.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.181
r_dihedral_angle_4_deg20.503
r_dihedral_angle_3_deg14.573
r_dihedral_angle_1_deg6.179
r_scangle_it5.485
r_scbond_it3.54
r_mcangle_it2.165
r_angle_refined_deg1.933
r_mcbond_it1.298
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.181
r_dihedral_angle_4_deg20.503
r_dihedral_angle_3_deg14.573
r_dihedral_angle_1_deg6.179
r_scangle_it5.485
r_scbond_it3.54
r_mcangle_it2.165
r_angle_refined_deg1.933
r_mcbond_it1.298
r_chiral_restr0.153
r_bond_refined_d0.023
r_gen_planes_refined0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4074
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms

Software

Software
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling