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Src family kinase Hck with bound inhibitor A-641359
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AD5 PDB ENTRY 1AD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 CRYSTALLIZATION CONDITIONS: HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-641359 [100 MM STOCK SOLUTION OF THE MALEIC ACID SALT IN DMSO) TO GIVE A FINAL A-641359 CONCENTRATION OF 1 MM. HCK/A-641359 WAS THEN MIXED WITH RESERVOIR SOLUTION (12% PEG 6000, 3% 1, 5-DIAMINOPENTANE, 20% GLYCEROL, 200 MM CA(OAC)2, 100 MM TRIS.HCL PH 8.0) AND EQUILBRATED AGAINST THE RESERVOIR SOLUTION BY VAPOR DIFFUSION (SITTING DROPS) AT 277 K.
Crystal Properties Matthews coefficient Solvent content 3.1 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.861 α = 90 b = 72.909 β = 95.87 c = 180.002 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 CCD MARRESEARCH 2002-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.14 50 75.6 0.08 13.6 3 52558 38.1
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) 1 2.14 2.22 24.7 0.25 3.3 1.8
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 PDB ENTRY 1AD5 2.15 20 46145 2440 70.8 0.197 0.194 0.1959 0.253 0.2563 RANDOM 63.67
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] 2.99 -0.98 -0.92 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 18.974 r_dihedral_angle_3_deg 17.593 r_dihedral_angle_1_deg 5.951 r_scangle_it 3.344 r_scbond_it 2.105 r_mcangle_it 1.475 r_angle_refined_deg 1.427 r_mcbond_it 0.873 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 18.974 r_dihedral_angle_3_deg 17.593 r_dihedral_angle_1_deg 5.951 r_scangle_it 3.344 r_scbond_it 2.105 r_mcangle_it 1.475 r_angle_refined_deg 1.427 r_mcbond_it 0.873 r_nbtor_refined 0.307 r_nbd_refined 0.205 r_metal_ion_refined 0.186 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6925 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing