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Kinase domain of MERTK in complex with compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 35% PEG 400, 0.2M MgCl2, 0.1M Tris
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.487 α = 90 b = 91.315 β = 100.78 c = 69.68 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 2.65 45.66 99.2 0.177 0.194 0.079 0.988 6.2 5.9 18384
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 2.65 2.78 99.4 1.055 1.158 0.469 0.673 5.9
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 4m3q 2.65 45.66 17465 903 99.13 0.2235 0.2218 0.2274 0.2574 0.2582 RANDOM 49.289
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] 3.3 0.32 -1.68 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 6.709 r_angle_refined_deg 1.382 r_angle_other_deg 1.167 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 6.709 r_angle_refined_deg 1.382 r_angle_other_deg 1.167 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3893 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 46
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing