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The structure of p38beta C119S, C162S in complex with a dihydroquinazolinone inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 12-14% PEG 3350, 0.12 M ammonium fluoride, 1% DMSO, 30 uM CTAB, 10-20 mM LiCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.184 α = 90 b = 158.823 β = 91.59 c = 60.874 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 100 CCD MAR CCD 165 mm 2002-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 1.00 APS 17-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 50 98.5 0.058 8.8 5.3 46456 45759 -3 32.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 92 0.263 1.6 3.5 4583
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 FOURIER SYNTHESIS THROUGHOUT 3GC8 2.05 30 43404 2309 98.52 0.22443 0.22173 0.2177 0.27531 0.2714 RANDOM 33.395
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] 0.13 0.06 -0.78 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.453 r_dihedral_angle_4_deg 17.75 r_dihedral_angle_3_deg 15.743 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.49 r_scbond_it 1.574 r_angle_refined_deg 1.315 r_mcangle_it 1.121 r_mcbond_it 0.623 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.453 r_dihedral_angle_4_deg 17.75 r_dihedral_angle_3_deg 15.743 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.49 r_scbond_it 1.574 r_angle_refined_deg 1.315 r_mcangle_it 1.121 r_mcbond_it 0.623 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.145 r_symmetry_metal_ion_refined 0.136 r_chiral_restr 0.09 r_metal_ion_refined 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5384 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing