2V7O | pdb_00002v7o

Crystal structure of human calcium-calmodulin-dependent protein kinase II gamma


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BDWPDB ENTRY 1BDW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.10M MAGNESIUM CHLORIDE, 0.1M HEPES PH7, 20% PEG6K, 10% ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.5950.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.703α = 90
b = 117.226β = 90
c = 75.968γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-07-15MSINGLE 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
12.2542.331000.1110.4418326
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)
12.252.371000.721.94.1

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 1BDW2.2535.62173889361000.1790.1760.180.2410.25RANDOM33.45
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]
1.6-0.43-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg18.818
r_dihedral_angle_3_deg14.653
r_dihedral_angle_1_deg6.366
r_angle_other_deg1.33
r_angle_refined_deg1.296
r_symmetry_vdw_refined0.259
r_symmetry_vdw_other0.192
r_symmetry_hbond_refined0.192
r_nbd_refined0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg18.818
r_dihedral_angle_3_deg14.653
r_dihedral_angle_1_deg6.366
r_angle_other_deg1.33
r_angle_refined_deg1.296
r_symmetry_vdw_refined0.259
r_symmetry_vdw_other0.192
r_symmetry_hbond_refined0.192
r_nbd_refined0.19
r_nbd_other0.18
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.132
r_nbtor_other0.089
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2417
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing