2JBO

Protein kinase MK2 in complex with an inhibitor (crystal form-1, soaking)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NY3PDB ENTRY 1NY3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.51.5-1.6M SODIUM POTASSIUM PHOSPHATE PH 4.5, 0.014M DEOXY-BIGCHAP. THE INHIBITOR WAS SOAKED INTO CRYSTALS GROWN INITIALLY FROM MK2-ADP
Crystal Properties
Matthews coefficientSolvent content
4.572.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 253.959α = 90
b = 253.959β = 90
c = 253.959γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
13.148.999.80.0827.17.81323287.6
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)
13.13.151000.6648.2

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1NY33.148.91248272299.70.2320.230.274RANDOM72.47
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.472
r_dihedral_angle_4_deg29.582
r_dihedral_angle_3_deg22.55
r_dihedral_angle_1_deg7.265
r_scangle_it3.51
r_scbond_it2.013
r_angle_refined_deg1.706
r_mcangle_it1.504
r_mcbond_it0.863
r_nbtor_refined0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.472
r_dihedral_angle_4_deg29.582
r_dihedral_angle_3_deg22.55
r_dihedral_angle_1_deg7.265
r_scangle_it3.51
r_scbond_it2.013
r_angle_refined_deg1.706
r_mcangle_it1.504
r_mcbond_it0.863
r_nbtor_refined0.336
r_symmetry_vdw_refined0.258
r_nbd_refined0.253
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.147
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms2385
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing