2W2C | pdb_00002w2c

STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM- CALMODULIN DEPENDENT PROTEIN KINASE II DELTA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HKXPDB ENTRIES 1HKX,2UX0,2F86
experimental modelPDB 2UX0PDB ENTRIES 1HKX,2UX0,2F86
experimental modelPDB 2F86PDB ENTRIES 1HKX,2UX0,2F86

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.630% PEG400, 0.1M CADMIUM CHLORIDE, 0.1M SODIUM ACETATE PH4.6
Crystal Properties
Matthews coefficientSolvent content
2.8657

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.546α = 90
b = 117.803β = 111.92
c = 160.761γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-07-24MSINGLE 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
12.744.8699.70.0811.64.632349284.77
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)
12.72.851000.762.34.6

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 ENTRIES 1HKX,2UX0,2F862.744.868546213499.50.2120.2110.220.2450.25RANDOM36.44
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]
-1.22-1.9-2.282.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.304
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg14.463
r_dihedral_angle_1_deg6.48
r_scangle_it3.508
r_scbond_it2.082
r_angle_refined_deg1.362
r_mcangle_it1.198
r_angle_other_deg0.898
r_mcbond_it0.608
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.304
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg14.463
r_dihedral_angle_1_deg6.48
r_scangle_it3.508
r_scbond_it2.082
r_angle_refined_deg1.362
r_mcangle_it1.198
r_angle_other_deg0.898
r_mcbond_it0.608
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
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_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 Atoms13912
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing