2VZ6

Structure of human calcium calmodulin dependent protein kinase type II alpha (CAMK2A) in complex with Indirubin E804


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V7OPDB ENTRY 2V7O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.512% PEG6000, 0.1M TRIS PH8.5
Crystal Properties
Matthews coefficientSolvent content
3.9869

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.244α = 90
b = 113.621β = 90
c = 131.868γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-01-26MSINGLE 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
12.349.881000.1211.14.95168737
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)
12.32.421000.782.34.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2V7O2.343.154934722691000.1650.1630.203RANDOM21.77
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]
3.58-0.76-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.262
r_dihedral_angle_4_deg20.773
r_dihedral_angle_3_deg14.716
r_scangle_it8.025
r_dihedral_angle_1_deg6.205
r_scbond_it5.907
r_mcangle_it3.535
r_mcbond_it2.177
r_angle_refined_deg1.569
r_angle_other_deg0.943
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.262
r_dihedral_angle_4_deg20.773
r_dihedral_angle_3_deg14.716
r_scangle_it8.025
r_dihedral_angle_1_deg6.205
r_scbond_it5.907
r_mcangle_it3.535
r_mcbond_it2.177
r_angle_refined_deg1.569
r_angle_other_deg0.943
r_symmetry_vdw_other0.29
r_nbd_other0.236
r_nbd_refined0.196
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.123
r_nbtor_other0.111
r_chiral_restr0.094
r_symmetry_vdw_refined0.073
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms4654
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing