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Human Kinase with pyrrole-indolinone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OL7 PDB ENTRY 1OL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10% PEG6000, 200 MM MGCL2. SITTING DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX.
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.634 α = 90 b = 56.924 β = 95.98 c = 66.012 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 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.2 65 99.7 0.09 16.8 8.2 15620 32.55
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 2.2 2.32 98.1 0.48 3.4 6.3
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 PDB ENTRY 1OL7 2.2 30 14883 796 99.7 0.217 0.214 0.2088 0.277 0.2714 RANDOM 33.55
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] 0.93 -1.77 -1.95 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.3 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 5.514 r_scangle_it 1.922 r_scbond_it 1.238 r_bond_other_d 1.225 r_mcangle_it 0.895 r_mcbond_it 0.552 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.3 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 5.514 r_scangle_it 1.922 r_scbond_it 1.238 r_bond_other_d 1.225 r_mcangle_it 0.895 r_mcbond_it 0.552 r_nbtor_refined 0.295 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_angle_refined_deg r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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 2014 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing