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Crystal structure of Src kinase domain in complex with CGP77675
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FMK 1FMK/3LCK hybrid experimental model PDB 3LCK 1FMK/3LCK hybrid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.53 α = 100.38 b = 62.95 β = 89.16 c = 72.79 γ = 89.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2002-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 20 96 0.053 9.9 29676
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.5 93.5 0.203 5.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FMK/3LCK hybrid 2.3 20 29675 1562 97.13 0.19585 0.19312 0.24746 RANDOM 41.462
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] -0.44 0.43 0.25 -0.42 -0.43 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.629 r_dihedral_angle_3_deg 16.437 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_1_deg 6.046 r_scangle_it 2.55 r_angle_refined_deg 1.688 r_scbond_it 1.649 r_mcangle_it 1.318 r_mcbond_it 0.857 r_angle_other_deg 0.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.629 r_dihedral_angle_3_deg 16.437 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_1_deg 6.046 r_scangle_it 2.55 r_angle_refined_deg 1.688 r_scbond_it 1.649 r_mcangle_it 1.318 r_mcbond_it 0.857 r_angle_other_deg 0.806 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.28 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.181 r_nbtor_refined 0.179 r_mcbond_other 0.141 r_nbtor_other 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.012 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 4091 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing