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Human P38 MAP kinase in complex with RL48
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, HANGING DROP 5.9 293 100 mM MES, 20-30% PEG 4000, 50 mM n-beta-octyl-glucoside, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.47 α = 90 b = 74.09 β = 93.76 c = 71.71 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Osmic 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54170
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 99.8 0.039 25.64 4.1 43150 43071 -3 36.277
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 99.9 0.248 6 4.02 5578
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 32.41 43070 1077 100 0.19 0.189 0.1894 0.235 0.2333 RANDOM 30.894
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] 0.65 -0.42 -0.29 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.576 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.053 r_scbond_it 2.044 r_angle_refined_deg 1.546 r_mcangle_it 1.481 r_mcbond_it 0.883 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.576 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.053 r_scbond_it 2.044 r_angle_refined_deg 1.546 r_mcangle_it 1.481 r_mcbond_it 0.883 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5420 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 168
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling