6CTH

Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UIMPDB entry 3UIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529318% PEG8000, 0.2 M magnesium acetate, 0.1 M SSB buffer
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.798α = 90
b = 56.798β = 90
c = 358.04γ = 120
Symmetry
Space GroupP 61 2 2

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
11.7301000.0810.0860.020.99917.418.639498
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)
11.71.7399.91.730.5440.8291.418.8

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 3UIM1.73037364197799.940.20980.208350.23846RANDOM41.402
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]
0.520.260.52-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.943
r_dihedral_angle_4_deg24.89
r_dihedral_angle_3_deg14.059
r_dihedral_angle_1_deg5.954
r_long_range_B_refined5.899
r_long_range_B_other5.856
r_scangle_other2.666
r_mcangle_it2.37
r_mcangle_other2.37
r_angle_refined_deg1.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.943
r_dihedral_angle_4_deg24.89
r_dihedral_angle_3_deg14.059
r_dihedral_angle_1_deg5.954
r_long_range_B_refined5.899
r_long_range_B_other5.856
r_scangle_other2.666
r_mcangle_it2.37
r_mcangle_other2.37
r_angle_refined_deg1.629
r_scbond_it1.619
r_scbond_other1.619
r_mcbond_it1.406
r_mcbond_other1.403
r_angle_other_deg1.013
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.009
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 Atoms2255
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing