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Human p38 MAP Kinase in Complex with RL113
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.95 α = 90 b = 69.85 β = 90 c = 74.71 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 90 CCD MARRESEARCH Dynamically bendable mirror 2009-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000000 SLS X10SA
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 3.4 40 99.2 0.159 12.06 3.85 5215 5175 -3 24.053
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) 3.4 3.5 100 0.439 4.7 3.93 424
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ZYJ 3.4 40 5215 5174 518 100 0.23 0.222 0.2182 0.305 0.2996 RANDOM 32.09
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] 2.1 0.55 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 19.639 r_dihedral_angle_4_deg 14.049 r_dihedral_angle_1_deg 5.803 r_angle_refined_deg 1.185 r_scangle_it 0.959 r_mcangle_it 0.621 r_scbond_it 0.539 r_mcbond_it 0.335 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 19.639 r_dihedral_angle_4_deg 14.049 r_dihedral_angle_1_deg 5.803 r_angle_refined_deg 1.185 r_scangle_it 0.959 r_mcangle_it 0.621 r_scbond_it 0.539 r_mcbond_it 0.335 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2661 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 55
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction