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P38 kinase crystal structure in complex with RO4499
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P38 PDB entry 1P38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 290 50 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.524 α = 90 b = 85.828 β = 90 c = 123.859 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 2.2 43 95.3 24218 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.3 2.9 3521
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 1P38 2.2 42.91 22981 1236 95.35 0.21179 0.21036 0.2064 0.23772 0.2342 RANDOM 28.6
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] -0.14 -0.55 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_1_deg 5.262 r_scangle_it 1.789 r_scbond_it 1.125 r_mcangle_it 1.038 r_angle_refined_deg 1.031 r_mcbond_it 0.583 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_1_deg 5.262 r_scangle_it 1.789 r_scbond_it 1.125 r_mcangle_it 1.038 r_angle_refined_deg 1.031 r_mcbond_it 0.583 r_nbtor_refined 0.299 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement