2JII

Structure of vaccinia related kinase 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherENSEMBLE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES PH=7.5 2.0 M AMMONIUMFORMATE, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.258α = 90
b = 54.423β = 91.22
c = 91.822γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1246.899.20.0612.53.660969
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.195.40.422.22.6

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 REPLACEMENTTHROUGHOUTENSEMBLE25057853309299.40.1810.1790.223RANDOM27.82
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]
-0.030.27-1.271.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.591
r_dihedral_angle_4_deg17.843
r_dihedral_angle_3_deg13.809
r_scangle_it7.95
r_scbond_it6.364
r_dihedral_angle_1_deg5.975
r_mcangle_it4.014
r_mcbond_it3.047
r_angle_refined_deg1.265
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.591
r_dihedral_angle_4_deg17.843
r_dihedral_angle_3_deg13.809
r_scangle_it7.95
r_scbond_it6.364
r_dihedral_angle_1_deg5.975
r_mcangle_it4.014
r_mcbond_it3.047
r_angle_refined_deg1.265
r_angle_other_deg0.93
r_symmetry_vdw_other0.201
r_nbd_refined0.195
r_nbd_other0.183
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.164
r_symmetry_vdw_refined0.134
r_symmetry_hbond_refined0.114
r_nbtor_other0.084
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms5111
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing