2WEL | pdb_00002wel

Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VN9PDB ENTRIES 2VN9, 1MXE
experimental modelPDB 1MXEPDB ENTRIES 2VN9, 1MXE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M SODIUM POTASSIUM PHOSPHATE, 20% PEG3350 10% ETHYLENE GLYCOL, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.652.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.26α = 90
b = 68.85β = 90
c = 121.98γ = 90
Symmetry
Space GroupP 21 21 21

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
11.933.1399.70.1110.84.94590120.729
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)
11.921000.82.64.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 2VN9, 1MXE1.933.344507482799.570.16130.160570.180.199290.21RANDOM16.066
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]
-1.921.020.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.518
r_dihedral_angle_4_deg18.403
r_dihedral_angle_3_deg12.972
r_scangle_it9.372
r_scbond_it7.07
r_dihedral_angle_1_deg5.207
r_mcangle_it4.709
r_mcbond_it3.306
r_angle_refined_deg1.37
r_mcbond_other1.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.518
r_dihedral_angle_4_deg18.403
r_dihedral_angle_3_deg12.972
r_scangle_it9.372
r_scbond_it7.07
r_dihedral_angle_1_deg5.207
r_mcangle_it4.709
r_mcbond_it3.306
r_angle_refined_deg1.37
r_mcbond_other1.101
r_angle_other_deg0.911
r_symmetry_hbond_refined0.23
r_nbd_refined0.216
r_nbtor_refined0.177
r_nbd_other0.17
r_symmetry_vdw_other0.17
r_metal_ion_refined0.163
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.156
r_xyhbond_nbd_other0.096
r_nbtor_other0.087
r_chiral_restr0.085
r_symmetry_hbond_other0.047
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_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 Atoms3544
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing