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Apo crystal structure of the MerTK kinase domain
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 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.621 α = 90 b = 91.604 β = 90 c = 71.623 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 2019-12-05 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 1.739 48.044 93.2 0.051 0.055 0.022 1 16.3 6.6 17430
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 1.739 1.983 67.3 0.896 0.984 0.401 0.709 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 1.74 48.044 16594 820 55.56 0.2022 0.2001 0.2076 0.2465 0.2058 RANDOM 42.019
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] 0.24 0.28 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 16.947 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 5.161 r_angle_refined_deg 1.319 r_angle_other_deg 0.936 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 16.947 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 5.161 r_angle_refined_deg 1.319 r_angle_other_deg 0.936 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2141 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction