☰ Navigation Tabs
Human P38 MAP kinase in complex with RL45
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 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.56 α = 90 b = 74.79 β = 90 c = 76.82 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 2008-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978030 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 2 50 99.5 0.071 19.12 5.43 26560 26431 -3 39.261
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 2.1 97.6 0.381 4.55 5.09 3552
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 41.74 26429 793 100 0.219 0.217 0.2164 0.27 0.2709 RANDOM 35.851
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] -0.08 -0.61 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_4_deg 14.943 r_dihedral_angle_1_deg 5.842 r_scangle_it 3.43 r_scbond_it 2.318 r_mcangle_it 1.749 r_angle_refined_deg 1.496 r_mcbond_it 1.025 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_4_deg 14.943 r_dihedral_angle_1_deg 5.842 r_scangle_it 3.43 r_scbond_it 2.318 r_mcangle_it 1.749 r_angle_refined_deg 1.496 r_mcbond_it 1.025 r_nbtor_refined 0.309 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2716 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XSCALE data scaling