3GGF | pdb_00003ggf

Crystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CKXPDB ENTRY 3CKX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277.1512%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.4249.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.92α = 90
b = 91.25β = 90
c = 108.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR225 CCDDynamically bendable mirror2009-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.8800SLSX10SA

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
12.3546.781000.13994.628094280942
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)
2.352.481000.84924.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3CKX2.3546.782804426636140899.930.221680.218790.230.276980.29RANDOM18.182
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]
-0.570.550.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.494
r_dihedral_angle_4_deg17.788
r_sphericity_bonded17.276
r_dihedral_angle_3_deg15.57
r_rigid_bond_restr6.59
r_dihedral_angle_1_deg6.112
r_sphericity_free5.558
r_scangle_it4.543
r_scbond_it2.548
r_mcangle_it1.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.494
r_dihedral_angle_4_deg17.788
r_sphericity_bonded17.276
r_dihedral_angle_3_deg15.57
r_rigid_bond_restr6.59
r_dihedral_angle_1_deg6.112
r_sphericity_free5.558
r_scangle_it4.543
r_scbond_it2.548
r_mcangle_it1.843
r_angle_refined_deg1.477
r_mcbond_it0.969
r_angle_other_deg0.951
r_mcbond_other0.255
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4287
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms65

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling