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P38 kinase crystal structure in complex with RO7125
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 2.9 57.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.461 α = 90 b = 87.215 β = 90 c = 124.869 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 ADSC QUANTUM 315 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) R Sym 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 50 98.1 0.128 33873 30.7
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 2 2.07 87.4 0.549 1.8 2985
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 33.86 31709 1685 97.11 0.21456 0.21311 0.2124 0.2421 0.241 RANDOM 30.469
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] -0.78 -0.28 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_3_deg 12.38 r_dihedral_angle_1_deg 5.133 r_scangle_it 1.864 r_scbond_it 1.15 r_mcangle_it 0.99 r_angle_refined_deg 0.982 r_mcbond_it 0.581 r_nbtor_refined 0.301 r_nbd_refined 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_3_deg 12.38 r_dihedral_angle_1_deg 5.133 r_scangle_it 1.864 r_scbond_it 1.15 r_mcangle_it 0.99 r_angle_refined_deg 0.982 r_mcbond_it 0.581 r_nbtor_refined 0.301 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing