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Structure of human p38alpha with N-[4-methyl-3-(6-{[2-(1-methylpyrrolidin-2-yl)ethyl]amino}pyridine-3-amido)phenyl]-2-(morpholin-4-yl)pyridine-4-carboxamide
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, SITTING DROP 7.4 296 14-16%(w/v) PEG8000, 300mM Magnesium acetate, 100mM Hepes pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.427 α = 90 b = 84.354 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 IMAGE PLATE RIGAKU RAXIS IV++ VARIMAX MIRRORS 2004-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 1.8 62.76 98.9 0.05 11.6 3.26 45051 1.9 30
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) 1.8 1.86 92.7 0.296 2.3 1.81 4463
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1WFC 1.8 16.72 42359 2245 97.36 0.18997 0.18772 0.23289 0.2201 RANDOM 27.941
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] -0.47 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 18.43 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 6.128 r_scangle_it 5.288 r_scbond_it 3.462 r_mcangle_it 2.56 r_angle_refined_deg 2.118 r_mcbond_it 1.497 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 18.43 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 6.128 r_scangle_it 5.288 r_scbond_it 3.462 r_mcangle_it 2.56 r_angle_refined_deg 2.118 r_mcbond_it 1.497 r_chiral_restr 0.166 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2826 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 60
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling