2V62 | pdb_00002v62

Structure of vaccinia-related kinase 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JIIPDB ENTRY 2JII

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.1 M SUCCINIC ACID PH=7.0 15% PEG3350
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.655α = 90
b = 157.532β = 90
c = 56.288γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-05-10MSINGLE 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
11.745.896.90.0615.35.867759
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)
11.71.893.30.592.35.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JII1.75064302341396.90.2030.2010.210.2360.24RANDOM26.73
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]
0.28-0.830.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.469
r_dihedral_angle_4_deg16.691
r_dihedral_angle_3_deg13.311
r_scangle_it8.803
r_scbond_it7.114
r_dihedral_angle_1_deg5.602
r_mcangle_it4.59
r_mcbond_it3.326
r_angle_refined_deg1.483
r_angle_other_deg1.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.469
r_dihedral_angle_4_deg16.691
r_dihedral_angle_3_deg13.311
r_scangle_it8.803
r_scbond_it7.114
r_dihedral_angle_1_deg5.602
r_mcangle_it4.59
r_mcbond_it3.326
r_angle_refined_deg1.483
r_angle_other_deg1.012
r_symmetry_vdw_other0.295
r_nbd_refined0.198
r_nbd_other0.191
r_symmetry_vdw_refined0.185
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.158
r_chiral_restr0.09
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4756
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing