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Conformational plasticity of p38 MAP kinase DFG mutants in response to inhibitor binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYJ PDB entry 1ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 10-15% PEG 4000, 0.1M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.319 α = 90 b = 69.839 β = 90 c = 76.088 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 93 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002+ 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 33.41 99.1 0.092 0.084 11.2 5.19 25143 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 96.1 4.2 4.59
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 1ZYJ 2.4 33.41 13626 1138 99.84 0.22019 0.2149 0.2137 0.28673 0.2852 RANDOM 32.09
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] 2.31 -1.33 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_3_deg 21.54 r_dihedral_angle_4_deg 15.647 r_dihedral_angle_1_deg 6.819 r_scangle_it 3.093 r_scbond_it 1.983 r_angle_refined_deg 1.78 r_mcangle_it 1.625 r_mcbond_it 0.928 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_3_deg 21.54 r_dihedral_angle_4_deg 15.647 r_dihedral_angle_1_deg 6.819 r_scangle_it 3.093 r_scbond_it 1.983 r_angle_refined_deg 1.78 r_mcangle_it 1.625 r_mcbond_it 0.928 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2683 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 41
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling