☰ Navigation Tabs
p38 kinase Crystal structure in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HRB PDB ENTRY 3HRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22% PEG 3350, 0.2M NaCl, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.94 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.26 α = 90 b = 87.23 β = 90 c = 122.81 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 RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.8 20 90.1 0.11 11267
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 2.8 2.9 98.4 0.377 2.92
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 3HRB 2.8 19.93 11267 547 90.12 0.25902 0.25516 0.2543 0.33907 0.3287 RANDOM 40.425
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] -0.41 0.27 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 18.706 r_dihedral_angle_1_deg 6.228 r_scangle_it 1.623 r_angle_refined_deg 1.199 r_scbond_it 0.927 r_mcangle_it 0.857 r_angle_other_deg 0.855 r_mcbond_it 0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 18.706 r_dihedral_angle_1_deg 6.228 r_scangle_it 1.623 r_angle_refined_deg 1.199 r_scbond_it 0.927 r_mcangle_it 0.857 r_angle_other_deg 0.855 r_mcbond_it 0.455 r_chiral_restr 0.062 r_mcbond_other 0.053 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2725 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction