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Structure of human LCK kinase with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LCK PDB ENTRY 3LCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 1.8-2.5M AMMONIUM SULFATE, 0.1M BISTRIS, PH6.5,VAPOR DIFFUSION, SITTING DROP, 277 DEG K, PROTEIN STOCK AT 1.5 MG/ML
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.579 α = 90 b = 74.16 β = 90 c = 92.85 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE RIGAKU RAXIS IV++ 1998-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.8 30 94.2 0.111 0.111 10.4 3 7251 7251 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 95.7 0.261 0.261 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LCK 2.8 28.56 7251 7251 337 94.6 0.167 0.165 0.1645 0.223 0.2138 RANDOM 19.2
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] -6.95 -0.28 7.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.4 c_scangle_it 3.16 c_mcangle_it 2.36 c_scbond_it 2.03 c_mcbond_it 1.36 c_angle_deg 1 c_improper_angle_d 0.66 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.4 c_scangle_it 3.16 c_mcangle_it 2.36 c_scbond_it 2.03 c_mcbond_it 1.36 c_angle_deg 1 c_improper_angle_d 0.66 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 40
Software Software Software Name Purpose AMoRE phasing CNX refinement DENZO data reduction SCALEPACK data scaling