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Crystal structure of MerTK kinase domain in complex with UNC2025
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRB pdbid 3BRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.1M Tris pH 8.5, 4.3M NaCl
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.849 α = 90 b = 92.04 β = 90 c = 71.621 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2020-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
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 1.778 48.139 93.8 0.037 0.04 0.016 1 21 6.6 18168
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 1.778 1.962 64 1.075 1.181 0.483 0.635 5.8
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 pdbid 3BRB 1.78 48.139 17267 893 61.46 0.196 0.1933 0.2021 0.2497 0.2042 RANDOM 48.966
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] -0.02 0.34 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.429 r_dihedral_angle_4_deg 20.62 r_dihedral_angle_3_deg 14.944 r_dihedral_angle_1_deg 6.196 r_angle_refined_deg 1.517 r_angle_other_deg 0.979 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.429 r_dihedral_angle_4_deg 20.62 r_dihedral_angle_3_deg 14.944 r_dihedral_angle_1_deg 6.196 r_angle_refined_deg 1.517 r_angle_other_deg 0.979 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2124 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 47
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction