6BQP

Crystal Structure of the Human CAMKK2B in complex with Crenolanib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UYJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729322% PEG 3350; 0.21 M Ammonium Acetate; 0.1M CHC buffer pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2745.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.113α = 90
b = 77.834β = 90
c = 78.709γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979100APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9519.8999.80.0480.0570.030.99918.96.422637
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95299.90.8980.5530.7531.96.7

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 REPLACEMENTTHROUGHOUT5UYJ1.9519.8921450114299.740.191250.189220.22666RANDOM39.761
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]
-2.42-0.352.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.77
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg12.492
r_dihedral_angle_1_deg5.827
r_long_range_B_other5.25
r_long_range_B_refined5.246
r_scangle_other2.735
r_mcangle_it2.149
r_mcangle_other2.149
r_scbond_it1.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.77
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg12.492
r_dihedral_angle_1_deg5.827
r_long_range_B_other5.25
r_long_range_B_refined5.246
r_scangle_other2.735
r_mcangle_it2.149
r_mcangle_other2.149
r_scbond_it1.757
r_scbond_other1.754
r_angle_refined_deg1.641
r_mcbond_it1.376
r_mcbond_other1.376
r_angle_other_deg0.995
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2034
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing