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P38 kinase crystal structure in complex with RO9552
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 2.91 57.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.035 α = 90 b = 86.233 β = 90 c = 125.508 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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 95.6 0.065 32876 37.1
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 92.3 0.595 1.9 3096
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 34.1 31168 1655 95.36 0.22051 0.21876 0.217 0.25391 0.2444 RANDOM 39.686
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] -0.79 -0.09 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_dihedral_angle_4_deg 18.33 r_dihedral_angle_3_deg 12.463 r_dihedral_angle_1_deg 5.003 r_scangle_it 1.926 r_scbond_it 1.199 r_mcangle_it 1.067 r_angle_refined_deg 1.002 r_mcbond_it 0.617 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_dihedral_angle_4_deg 18.33 r_dihedral_angle_3_deg 12.463 r_dihedral_angle_1_deg 5.003 r_scangle_it 1.926 r_scbond_it 1.199 r_mcangle_it 1.067 r_angle_refined_deg 1.002 r_mcbond_it 0.617 r_nbtor_refined 0.303 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing