2CDZ

CRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4 IN COMPLEX WITH CGP74514A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVAPDB ENTRY 2BVA

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.564.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.817α = 90
b = 145.817β = 90
c = 42.382γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2005-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
12.25098.70.0712.96.76235903
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)
12.22.392.20.4145.67

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BVA2.3103.1419821106099.60.2020.20.248RANDOM30.41
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]
-1.56-1.563.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.36
r_dihedral_angle_4_deg17.733
r_dihedral_angle_3_deg16.226
r_scangle_it6.17
r_dihedral_angle_1_deg5.499
r_scbond_it4.483
r_mcangle_it2.558
r_mcbond_it1.713
r_angle_refined_deg1.43
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.36
r_dihedral_angle_4_deg17.733
r_dihedral_angle_3_deg16.226
r_scangle_it6.17
r_dihedral_angle_1_deg5.499
r_scbond_it4.483
r_mcangle_it2.558
r_mcbond_it1.713
r_angle_refined_deg1.43
r_angle_other_deg0.941
r_symmetry_vdw_other0.284
r_symmetry_hbond_refined0.229
r_nbd_other0.197
r_nbd_refined0.192
r_symmetry_vdw_refined0.191
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.165
r_nbtor_other0.089
r_chiral_restr0.07
r_bond_refined_d0.012
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_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 Atoms2246
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing