☰ Navigation Tabs
Human p38 MAP Kinase in Complex with RL51
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 5.6 293 100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.64 α = 90 b = 74.06 β = 93.9 c = 72 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 90 CCD MARRESEARCH Dynamically bendable mirror 2009-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.977032 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 2.6 40 99.5 0.111 19.13 3.5 22992 22870 -3 36.301
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 2.6 2.7 99.3 0.499 5.4 3.49 2455
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 2.6 40 22992 22868 915 99.5 0.197 0.194 0.1995 0.271 0.2693 RANDOM 17.587
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] 0.5 -1.14 -0.94 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_3_deg 19.223 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_1_deg 6.338 r_scangle_it 2.641 r_scbond_it 1.677 r_angle_refined_deg 1.598 r_mcangle_it 1.484 r_mcbond_it 0.827 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_3_deg 19.223 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_1_deg 6.338 r_scangle_it 2.641 r_scbond_it 1.677 r_angle_refined_deg 1.598 r_mcangle_it 1.484 r_mcbond_it 0.827 r_nbtor_refined 0.317 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5432 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 148
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling