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Mutagenesis of p38 MAP kinase establishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-out state
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 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.52 α = 90 b = 73.85 β = 90 c = 76.09 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 2004-08-16 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 2.2 40 96.7 0.083 0.055 7.1 19105
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) 2.2 2.37 96.2 0.441 0.426 2 3740
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 2.2 23.99 16655 1420 91.68 0.23728 0.23257 0.2314 0.29322 0.2959 RANDOM 29.034
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] -0.46 -0.86 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.22 r_dihedral_angle_3_deg 20.08 r_dihedral_angle_4_deg 18.925 r_dihedral_angle_1_deg 6.771 r_scangle_it 4.374 r_scbond_it 2.745 r_mcangle_it 1.843 r_angle_refined_deg 1.783 r_mcbond_it 0.996 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.22 r_dihedral_angle_3_deg 20.08 r_dihedral_angle_4_deg 18.925 r_dihedral_angle_1_deg 6.771 r_scangle_it 4.374 r_scbond_it 2.745 r_mcangle_it 1.843 r_angle_refined_deg 1.783 r_mcbond_it 0.996 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2703 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing