☰ Navigation Tabs
p38alpha bound to novel DGF-out compound PF-00215955
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GFS PDB ENTRY 2GFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 The compound 2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine is required to obtain the crystal form.
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.031 α = 90 b = 74.878 β = 90 c = 77.617 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 CCD MAR CCD 165 mm 165MM-DIAMETER CIRCULAR APERTURE, 0.79 MICRON PIXELS ON THE PHOSPHOR M SINGLE WAVELENGTH 2 1 x-ray
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM APS 17-BM 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 53.8 41644 20.5
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) 1.7 1.76 72.7 0.304 2.9
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 2GFS 1.7 53.8 39548 2094 97.5 0.196 0.194 0.1942 0.242 0.2422 RANDOM 26.56
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] -0.06 -0.15 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 21.201 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_1_deg 5.137 r_scangle_it 3.771 r_scbond_it 2.508 r_mcangle_it 1.657 r_angle_refined_deg 1.405 r_mcbond_it 1.052 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 21.201 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_1_deg 5.137 r_scangle_it 3.771 r_scbond_it 2.508 r_mcangle_it 1.657 r_angle_refined_deg 1.405 r_mcbond_it 1.052 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 2694 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling PHASER phasing