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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 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.44 α = 90 b = 73.88 β = 90 c = 76.03 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 78.2 0.12 0.094 7.5 21427 15280
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 83.4 0.397 0.388 2.5 3198
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 24.7 16691 1430 92.96 0.23511 0.23002 0.2305 0.29583 0.2975 RANDOM 26.122
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] -0.43 -0.87 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.733 r_dihedral_angle_4_deg 21.499 r_dihedral_angle_3_deg 19.833 r_dihedral_angle_1_deg 6.617 r_scangle_it 4.148 r_scbond_it 2.634 r_mcangle_it 1.794 r_angle_refined_deg 1.712 r_mcbond_it 0.98 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.733 r_dihedral_angle_4_deg 21.499 r_dihedral_angle_3_deg 19.833 r_dihedral_angle_1_deg 6.617 r_scangle_it 4.148 r_scbond_it 2.634 r_mcangle_it 1.794 r_angle_refined_deg 1.712 r_mcbond_it 0.98 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing