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Src kinase bound to eCF506 trapped in inactive conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 6% PEG3350, 300mM Ammonium acetate, 0.1M HEPES pH7.5, 10mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.03 39.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.778 α = 90 b = 62.594 β = 98 c = 51.442 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 PILATUS 6M 2018-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97912 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 50 99.4 0.067 0.043 0.998 11.7 3.3 41802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.539 99.52 0.763 0.493 0.626 3.3
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 4MXO 1.5 41.41 39589 2192 99.34 0.1818 0.18 0.1799 0.2133 0.2128 RANDOM 17.634
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] 0.1 -0.02 0.02 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 22.077 r_dihedral_angle_3_deg 12.74 r_dihedral_angle_1_deg 11.022 r_angle_refined_deg 1.613 r_angle_other_deg 1.497 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 22.077 r_dihedral_angle_3_deg 12.74 r_dihedral_angle_1_deg 11.022 r_angle_refined_deg 1.613 r_angle_other_deg 1.497 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 41
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction