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Crystal structure of p38 in complex with a biphenylamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1M ADA, 0.18M (NH4)2SO4, 18-20% PEG5000MME, 3-4% Jeffamine ED600, 2mM b-Mercaptoethanol.
, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.753 α = 90 b = 85.688 β = 90 c = 125.206 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++ MIRRORS 2001-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.5418
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 2.1 35 86.1 0.102 7.2 25525 27.8
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 2.1 2.18 86.1 0.542 2513
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1WFC 2.1 20 25431 1296 100 0.184 0.181 0.249 0.254 RANDOM 35.344
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] -0.48 -0.09 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 21.811 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 11.319 r_scangle_it 4.385 r_scbond_it 3.022 r_mcangle_it 1.875 r_angle_refined_deg 1.61 r_mcbond_it 1.063 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 21.811 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 11.319 r_scangle_it 4.385 r_scbond_it 3.022 r_mcangle_it 1.875 r_angle_refined_deg 1.61 r_mcbond_it 1.063 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2803 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing