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Crystal structure of p38alpha C162S in complex with SB20358 and CAS 2094667-81-7 (behind catalytic site; Y35 in), P 21 21 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.087 M Ca Acetate
0.1M MES pH 6.0
7.1% PEG 550MME
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.142 α = 90 b = 74.57 β = 90 c = 77.55 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 PIXEL DECTRIS PILATUS 6M Elliptically bent mirror 2020-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
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 2.25 77.55 100 0.092 16.5 5.6 18525 28.9
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 2.25 2.37 100 0.451 9.2 5.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4LOO 2.25 53.752 18480 884 99.957 0.195 0.1929 0.1987 0.2479 0.2508 random 36.604
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] -0.918 -1.492 2.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.399 r_dihedral_angle_6_deg 13.867 r_lrange_it 6.405 r_lrange_other 6.329 r_dihedral_angle_1_deg 5.721 r_dihedral_angle_2_deg 4.757 r_scangle_it 3.968 r_scangle_other 3.967 r_mcangle_it 3.813 r_mcangle_other 3.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.399 r_dihedral_angle_6_deg 13.867 r_lrange_it 6.405 r_lrange_other 6.329 r_dihedral_angle_1_deg 5.721 r_dihedral_angle_2_deg 4.757 r_scangle_it 3.968 r_scangle_other 3.967 r_mcangle_it 3.813 r_mcangle_other 3.812 r_scbond_it 2.304 r_scbond_other 2.304 r_mcbond_it 2.257 r_mcbond_other 2.255 r_angle_refined_deg 1.182 r_angle_other_deg 0.409 r_nbd_refined 0.214 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.18 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.146 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.05 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2824 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing