5LMA

HUMAN SPLEEN TYROSINE KINASE KINASE DOMAIN IN COMPLEX WITH AZANAPHTHYRIDINE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house coordinates

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG3350, Sodium formate.
Crystal Properties
Matthews coefficientSolvent content
2.1141.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.175α = 90
b = 87.454β = 99.64
c = 39.851γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4343.73960.0320.99920.43.14680315.524
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.5185.90.1070.9785.72.1

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 SYNTHESISTHROUGHOUTIn-house coordinates1.432044455230695.820.15730.15590.183RANDOM18.816
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]
0.520.29-0.43-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.258
r_dihedral_angle_4_deg16.493
r_dihedral_angle_3_deg10.428
r_dihedral_angle_1_deg4.283
r_mcangle_it2.037
r_mcbond_it1.32
r_mcbond_other1.318
r_angle_refined_deg1.188
r_angle_other_deg0.736
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.258
r_dihedral_angle_4_deg16.493
r_dihedral_angle_3_deg10.428
r_dihedral_angle_1_deg4.283
r_mcangle_it2.037
r_mcbond_it1.32
r_mcbond_other1.318
r_angle_refined_deg1.188
r_angle_other_deg0.736
r_chiral_restr0.081
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2184
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms39

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing