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Src family kinase Hck with bound inhibitor A-770041
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 HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-770041 [100 MM STOCK SOLUTION IN DMSO) TO GIVE A FINAL A-770041 CONCENTRATION OF 1 MM. HCK/A-770041 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 = 49.015 α = 90 b = 73.176 β = 95.52 c = 180.167 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 IMAGE PLATE MARRESEARCH OSMIC DUAL MIRRORS 2003-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.85 50 96.1 0.09 9.3 3.2 28918 74.3
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 2.85 2.95 78.1 0.39 2.5 2.7
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 2.85 40 27348 1440 96.2 0.204 0.2 0.1985 0.273 0.2684 RANDOM 51.89
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] 6.29 -3.19 -1.3 -5.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_3_deg 20.623 r_dihedral_angle_4_deg 19.645 r_dihedral_angle_1_deg 6.884 r_scangle_it 2.524 r_angle_refined_deg 1.648 r_scbond_it 1.497 r_mcangle_it 1.075 r_mcbond_it 0.608 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_3_deg 20.623 r_dihedral_angle_4_deg 19.645 r_dihedral_angle_1_deg 6.884 r_scangle_it 2.524 r_angle_refined_deg 1.648 r_scbond_it 1.497 r_mcangle_it 1.075 r_mcbond_it 0.608 r_nbtor_refined 0.322 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.166 r_metal_ion_refined 0.164 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 6992 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing