☰ Navigation Tabs
Human p38 MAP Kinase in Complex with RL38
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 5.8 293 100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.71 α = 90 b = 74.52 β = 90 c = 78.91 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 100 IMAGE PLATE MAR scanner 300 mm plate Osmic 2008-05-06 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 2.4 40 99.9 0.069 17.1 4.8 15943 15927 -3 39.99
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) 2.4 2.53 100 0.357 5.2 4.8 2264
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 PDB entry 1ZYJ 2.4 34.87 15943 15869 953 99.5 0.208 0.203 0.2027 0.279 0.2777 RANDOM 26.959
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] -0.12 -0.35 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.976 r_dihedral_angle_4_deg 19.869 r_dihedral_angle_3_deg 18.719 r_dihedral_angle_1_deg 6.348 r_scangle_it 3.294 r_scbond_it 2.147 r_angle_refined_deg 1.62 r_mcangle_it 1.577 r_mcbond_it 0.907 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.976 r_dihedral_angle_4_deg 19.869 r_dihedral_angle_3_deg 18.719 r_dihedral_angle_1_deg 6.348 r_scangle_it 3.294 r_scbond_it 2.147 r_angle_refined_deg 1.62 r_mcangle_it 1.577 r_mcbond_it 0.907 r_nbtor_refined 0.313 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.171 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2660 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 50
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling MOSFLM data reduction SCALA data scaling