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Human p38 MAP Kinase in Complex with Dasatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.06 α = 90 b = 69.78 β = 90 c = 74.57 γ = 90
Symmetry Space Group P 21 21 21
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 MAR scanner 300 mm plate Osmic 2009-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54170
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 2.1 40 97.6 0.035 29.6 4.15 21650 21132 -3 30.919
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) 2.1 2.2 95.9 0.16 9.4 4.11 2783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ZYJ 2.1 40 21650 21131 846 100 0.204 0.202 0.2034 0.254 0.2531 RANDOM 25.44
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] 1.84 -0.85 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.545 r_dihedral_angle_3_deg 16.92 r_dihedral_angle_4_deg 16.087 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.446 r_scbond_it 2.159 r_mcangle_it 1.496 r_angle_refined_deg 1.456 r_mcbond_it 0.807 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.545 r_dihedral_angle_3_deg 16.92 r_dihedral_angle_4_deg 16.087 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.446 r_scbond_it 2.159 r_mcangle_it 1.496 r_angle_refined_deg 1.456 r_mcbond_it 0.807 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2673 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 53
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction