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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% PEG4000, 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 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.489 α = 90 b = 70.724 β = 90 c = 75.682 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 37.84 90.8 0.05 0.046 30 4.5 25513 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 2.15 93.4 5 4.4 4677
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ZYJ 2 37.84 21329 1791 90.81 0.22911 0.22478 0.2275 0.28162 RANDOM 35.497
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] 1.53 -0.42 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.48 r_dihedral_angle_4_deg 19.963 r_dihedral_angle_3_deg 19.33 r_dihedral_angle_1_deg 6.047 r_scangle_it 2.737 r_scbond_it 1.762 r_mcangle_it 1.463 r_angle_refined_deg 1.454 r_mcbond_it 0.841 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.48 r_dihedral_angle_4_deg 19.963 r_dihedral_angle_3_deg 19.33 r_dihedral_angle_1_deg 6.047 r_scangle_it 2.737 r_scbond_it 1.762 r_mcangle_it 1.463 r_angle_refined_deg 1.454 r_mcbond_it 0.841 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2676 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 41
Software Software Software Name Purpose APEX data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling