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Crystal structure of P38 in complex with biphenyl amide inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.57 α = 90 b = 86.106 β = 90 c = 124.362 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 2000-05-19 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 2.5 40 87 0.096 12.2 15373 45.382
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 2.5 2.59 77.1 0.427 1.7 1308
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.5 20 15289 763 100 0.172 0.169 0.1721 0.239 0.2385 RANDOM 34.4
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] 1.12 -1.95 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 18.553 r_dihedral_angle_3_deg 13.904 r_dihedral_angle_1_deg 4.327 r_scangle_it 3.538 r_scbond_it 2.347 r_mcangle_it 1.687 r_angle_refined_deg 1.444 r_mcbond_it 0.953 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 18.553 r_dihedral_angle_3_deg 13.904 r_dihedral_angle_1_deg 4.327 r_scangle_it 3.538 r_scbond_it 2.347 r_mcangle_it 1.687 r_angle_refined_deg 1.444 r_mcbond_it 0.953 r_nbtor_refined 0.309 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2791 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction