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Conformational plasticity of p38 MAP kinase DFG motif 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 10-20% PEG 4000, 0.1 M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.471 α = 90 b = 74.144 β = 90 c = 77.184 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 CCD ADSC QUANTUM 4 Mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.98 NSLS X4A
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 2.1 40 95 0.042 0.031 31 22530 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 79.6 0.266 0.236 2.9 2.4 1755
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 2.1 30.34 20146 1691 97.11 0.23502 0.23043 0.2291 0.28933 0.2898 RANDOM 36.33
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] 0.1 -1.32 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_3_deg 20.188 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_1_deg 6.552 r_scangle_it 3 r_scbond_it 1.984 r_mcangle_it 1.55 r_angle_refined_deg 1.467 r_mcbond_it 0.89 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_3_deg 20.188 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_1_deg 6.552 r_scangle_it 3 r_scbond_it 1.984 r_mcangle_it 1.55 r_angle_refined_deg 1.467 r_mcbond_it 0.89 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 47
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling