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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 5H3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES pH6.5, 18% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.838 α = 90 b = 90.838 β = 90 c = 197.107 γ = 90
Symmetry Space Group P 41 21 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 2015-11-04 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) Rrim I (All) Rpim I (All) 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 2.54 66.87 100 0.348 0.363 0.103 0.994 7 12.1 28231
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 2.54 2.61 99.9 2.872 3.029 0.951 0.563 9.8
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 5H3Q 2.54 66.79 26588 1369 99.13 0.22793 0.22486 0.2294 0.28737 0.2827 RANDOM 64.019
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] 0.71 0.71 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.223 r_dihedral_angle_4_deg 16.813 r_dihedral_angle_3_deg 16.771 r_dihedral_angle_1_deg 7.93 r_long_range_B_refined 6.771 r_long_range_B_other 6.76 r_scangle_other 3.357 r_mcangle_it 3.138 r_mcangle_other 3.138 r_scbond_it 1.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.223 r_dihedral_angle_4_deg 16.813 r_dihedral_angle_3_deg 16.771 r_dihedral_angle_1_deg 7.93 r_long_range_B_refined 6.771 r_long_range_B_other 6.76 r_scangle_other 3.357 r_mcangle_it 3.138 r_mcangle_other 3.138 r_scbond_it 1.982 r_scbond_other 1.981 r_angle_refined_deg 1.948 r_mcbond_it 1.871 r_mcbond_other 1.869 r_angle_other_deg 1.236 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4222 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing