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P38 kinase crystal structure in complex with RO2530
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 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.866 α = 90 b = 86.559 β = 90 c = 124.781 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 98.8 0.047 4.6 39535 29.4
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 94.9 0.496 2.1 3.6 3731
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 43.27 37306 1971 98.17 0.2057 0.20376 0.2031 0.24188 0.2403 RANDOM 30.923
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] -0.67 -0.3 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_1_deg 4.645 r_scangle_it 1.757 r_angle_refined_deg 1.114 r_scbond_it 1.052 r_mcangle_it 0.968 r_mcbond_it 0.542 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_1_deg 4.645 r_scangle_it 1.757 r_angle_refined_deg 1.114 r_scbond_it 1.052 r_mcangle_it 0.968 r_mcbond_it 0.542 r_nbtor_refined 0.299 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.11 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.062 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 2756 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing