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HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 Well Ingredients:
Precipitant: 20.0 %v/v (5.0 uL of stock 100.0 %v/v) Ethylene glycol
Precipitant: 10.0 %w/v (5.0 uL of stock 50.0 %w/v) PEG 4000
Salt: 0.1 M (0.5 uL of stock 5.0 M) Sodium chloride
Buffer: 0.1 M (2.5 uL of stock 1.0 M) MES (pH 6.00)
Plate setup temperature: 13 C
Plate incubation temperature: 13 C
Drop volume from well: 0.13 uL
Drop protein volume: 0.21045454545454545 uL
Protein concentration 15mg/ml
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.73 α = 90 b = 68.28 β = 104.56 c = 72.15 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER2 S 9M 2020-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.46 69.83 89.7 0.998 14.8 6.9 67520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.64 0.506
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.464 69.83 67520 3434 61.6 0.2164 0.215 0.2422 0.268 RANDOM 33.82
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] 0.4628 0.1499 0.3373 -0.8001
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.34 t_omega_torsion 3.25 t_angle_deg 0.98 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4534 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 106
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling BUSTER phasing