2J51

Crystal structure of Human STE20-like kinase bound to 5-Amino-3-((4-(aminosulfonyl)phenyl)amino) -N-(2,6-difluorophenyl)-1H-1,2,4-triazole- 1-carbothioamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U5RPDB ENTRY 1U5R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.516% PEG3350, 0.15M KSCN, 10% ETG, 0.1M BTP PH6.5, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
3.5365

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.195α = 90
b = 101.195β = 90
c = 177.173γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.162.261000.08168.93209440
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)
12.12.211000.812.78.9

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 1U5R2.1603043715891000.2020.2010.233RANDOM41.54
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]
-0.03-0.02-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.415
r_dihedral_angle_4_deg23.391
r_dihedral_angle_3_deg12.663
r_dihedral_angle_1_deg5.986
r_scangle_it2.795
r_scbond_it1.732
r_angle_refined_deg1.54
r_mcangle_it1.146
r_angle_other_deg1.095
r_mcbond_it0.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.415
r_dihedral_angle_4_deg23.391
r_dihedral_angle_3_deg12.663
r_dihedral_angle_1_deg5.986
r_scangle_it2.795
r_scbond_it1.732
r_angle_refined_deg1.54
r_mcangle_it1.146
r_angle_other_deg1.095
r_mcbond_it0.625
r_symmetry_vdw_other0.317
r_nbd_refined0.205
r_nbd_other0.188
r_symmetry_vdw_refined0.181
r_nbtor_refined0.17
r_mcbond_other0.14
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.123
r_nbtor_other0.087
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_other_d0.003
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_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 Atoms2250
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing