☰ 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 1OVE PDB ENTRY 1OVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22% PEG3350, 0.2 M sodium chloride, 1 mM THP, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.11 α = 90 b = 86.62 β = 90 c = 123.48 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++ 2006-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.2 19.79 93.3 0.08 2.97 25286 20902
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 2.2 2.28 96.1 0.41 3.03
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 1OVE 2.2 19.78 20902 1081 82.66 0.2649 0.2614 0.2523 0.3082 0.3115 RANDOM 39.6547
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] 0.15 -0.19 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.368 r_dihedral_angle_4_deg 25.979 r_dihedral_angle_3_deg 17.111 r_dihedral_angle_1_deg 7.199 r_scangle_it 3.735 r_scbond_it 2.488 r_angle_refined_deg 1.91 r_mcangle_it 1.661 r_mcbond_it 1.006 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.368 r_dihedral_angle_4_deg 25.979 r_dihedral_angle_3_deg 17.111 r_dihedral_angle_1_deg 7.199 r_scangle_it 3.735 r_scbond_it 2.488 r_angle_refined_deg 1.91 r_mcangle_it 1.661 r_mcbond_it 1.006 r_nbtor_refined 0.309 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2807 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing