X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JIFEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 3SO6Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 3G9WEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 3HQCEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 3DXEEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 2EJ8Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 2V76Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 1J0WEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 1WVHEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 2CY4Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 2DYQEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 1QQGEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 1X11Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC
experimental modelPDB 1AQCEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320% (w/v) PEG 6000, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
3.3763.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.938α = 90
b = 110.938β = 90
c = 315.255γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97926APS24-ID-E

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
12.75301000.1140.072317.93076893.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.851001.2119

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 REPLACEMENTTHROUGHOUTEnsemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC2.75329.66927776180990.430.22180.21980.2505Random102.7045
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
f_dihedral_angle_d12.692
f_angle_d0.868
f_chiral_restr0.046
f_bond_d0.004
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4418
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement