2VN9 | pdb_00002vn9

Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.6 M NAKPO4 HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8557

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.276α = 90
b = 68.276β = 90
c = 313.45γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-10-22MSINGLE 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
12.3451000.0910.74.639106258.2
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)
12.32.421000.5323.7

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 2V7O2.343.033704219601000.2130.2110.210.2480.25RANDOM51.32
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]
1.150.571.15-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.025
r_dihedral_angle_4_deg21.522
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg5.808
r_scangle_it5.576
r_scbond_it4.495
r_mcangle_it2.481
r_mcbond_it1.684
r_angle_refined_deg1.425
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.025
r_dihedral_angle_4_deg21.522
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg5.808
r_scangle_it5.576
r_scbond_it4.495
r_mcangle_it2.481
r_mcbond_it1.684
r_angle_refined_deg1.425
r_angle_other_deg0.976
r_mcbond_other0.87
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms4721
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing