6VZK

Crystal structure of human CaMKII-alpha (CAMK2A)kinase domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SOA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277PEG 6000, 50 mM HEPES, 3-Aminobenzene-sulfonic acid, 5-Sulfosalicylic acid dihydrate, p-Coumaric acid, PIPES, Terephthalic acid, Vanillic acid
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.147α = 90
b = 56.928β = 90
c = 97.461γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R 200K-ARigaku VariMax HF2019-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.555099.90.1950.2150.0933.55.58711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.751000.4890.8645.2

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 REPLACEMENTTHROUGHOUT3SOA2.5543.2871144699.810.21420.21030.2944RANDOM34.924
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]
0.91-2.431.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.242
r_dihedral_angle_4_deg22.288
r_dihedral_angle_3_deg19.46
r_dihedral_angle_1_deg8.705
r_angle_refined_deg1.589
r_angle_other_deg1.198
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.242
r_dihedral_angle_4_deg22.288
r_dihedral_angle_3_deg19.46
r_dihedral_angle_1_deg8.705
r_angle_refined_deg1.589
r_angle_other_deg1.198
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2075
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction