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Crystal Structure of TrkA kinase with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 1.2M Sodium Tartrate, 100mM Tris-HCl pH 8.5, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.97 68.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.845 α = 90 b = 157.195 β = 90 c = 52.306 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 49.1 99.67 0.114 13.98 6.6 32612
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 1.688
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 4F0I 2.1 46.81 32367 1704 99.48 0.1898 0.1884 0.199 0.2151 0.2219 RANDOM 45.184
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] 2.93 -0.98 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 15.033 r_dihedral_angle_1_deg 6.628 r_mcangle_it 5.561 r_mcbond_it 3.943 r_mcbond_other 3.942 r_angle_refined_deg 2.137 r_angle_other_deg 1.287 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_4_deg 15.033 r_dihedral_angle_1_deg 6.628 r_mcangle_it 5.561 r_mcbond_it 3.943 r_mcbond_other 3.942 r_angle_refined_deg 2.137 r_angle_other_deg 1.287 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2387 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing