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P38 kinase crystal structure in complex with 6-(2,4-Difluoro-phenoxy)-8-methyl-2-((R)-1-methyl-2-tetrazol-2-yl-ethylamino)-8H-pyrido[2,3-d]pyrimidin-7-one
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 57.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.654 α = 90 b = 85.914 β = 90 c = 126.37 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 1.0000 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 1.9 50 99.2 0.053 4.7 40153 32.1
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 1.9 1.97 98.4 0.625 2.15 4.4 3907
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 1.9 29.66 37747 1993 99.29 0.21845 0.21697 0.2153 0.24608 0.244 RANDOM 37.433
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] -1.62 0.58 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_1_deg 4.815 r_scangle_it 1.783 r_scbond_it 1.094 r_angle_refined_deg 1.049 r_mcangle_it 1.007 r_mcbond_it 0.585 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_1_deg 4.815 r_scangle_it 1.783 r_scbond_it 1.094 r_angle_refined_deg 1.049 r_mcangle_it 1.007 r_mcbond_it 0.585 r_nbtor_refined 0.298 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2801 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing