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Crystal structure of PTK6 Kinase domain with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.2 M tri-Lithium citrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.372 α = 90 b = 48.403 β = 105.14 c = 71.924 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2015-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 50 91.7 0.067 0.073 0.027 15.5 6.8 33176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 63.1 0.396 0.466 0.238 0.816 2.8 2061
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5D7V 1.7 50 28876 1548 91.78 0.1991 0.1974 0.1946 0.2302 0.2289 RANDOM 22.476
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] -0.85 0.36 0.4 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.519 r_dihedral_angle_4_deg 18.124 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 5.318 r_scangle_it 2.228 r_scbond_it 1.464 r_angle_refined_deg 1.274 r_mcangle_it 0.861 r_mcbond_it 0.519 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.519 r_dihedral_angle_4_deg 18.124 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 5.318 r_scangle_it 2.228 r_scbond_it 1.464 r_angle_refined_deg 1.274 r_mcangle_it 0.861 r_mcbond_it 0.519 r_nbtor_refined 0.305 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2126 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 52
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building