7M0K

HPK1 IN COMPLEX WITH COMPOUND 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2937% PEG 5K MNE, 0.05 M HEPES pH 6.5, Na3Cit pH 7, 20 mM Tris pH 8.0 , 150 mM NaCl , 5% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.074α = 90.02
b = 76.627β = 97.02
c = 89.2γ = 89.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim 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
12.0188.5394.70.0340.0450.99912.372.27474250.827
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.2692.60.4480.590.9982.152.2

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 REPLACEMENTTHROUGHOUTpreviously solved structure2.0188.5372002170493.40.24830.24770.278RANDOM80.406
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]
4.09-0.645.88-2.90.5-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.067
r_dihedral_angle_4_deg13.805
r_dihedral_angle_3_deg13.121
r_dihedral_angle_1_deg6.035
r_angle_refined_deg1.47
r_angle_other_deg1.19
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.067
r_dihedral_angle_4_deg13.805
r_dihedral_angle_3_deg13.121
r_dihedral_angle_1_deg6.035
r_angle_refined_deg1.47
r_angle_other_deg1.19
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9102
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms120

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing