☰ Navigation Tabs
Crystal Structure of P38 Kinase in Complex with a biphenyl amide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WFC PDB entry 1WFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 Authors suggest to see publication for details, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.96 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.63 α = 90 b = 86.103 β = 90 c = 124.811 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 2002-02-26 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 99.6 0.111 10.4 29415 26.5
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 99.1 0.573 2.3 2880
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 PDB entry 1WFC 2.1 20 29340 1491 100 0.177 0.174 0.1774 0.227 0.2285 RANDOM 35.533
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 -1.3 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.456 r_dihedral_angle_4_deg 24.909 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 10.83 r_scangle_it 4.432 r_scbond_it 3.168 r_mcangle_it 2.073 r_angle_refined_deg 1.431 r_mcbond_it 1.324 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.456 r_dihedral_angle_4_deg 24.909 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 10.83 r_scangle_it 4.432 r_scbond_it 3.168 r_mcangle_it 2.073 r_angle_refined_deg 1.431 r_mcbond_it 1.324 r_nbtor_refined 0.305 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2818 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing