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Crystal structure of p38 in complex with SR43
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 297.15 22.5% PEG Smear Medium, 0.1M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.349 α = 90 b = 74.83 β = 90 c = 77.199 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 PILATUS3 6M 2016-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 77.199 99.9 0.071 0.078 0.032 0.999 12.7 5.9 30526
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.8 0.844 0.844 0.927 0.377 0.625 2 5.8
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 MOLECULAR REPLACEMENT THROUGHOUT 5lar 1.9 53.73 28854 1610 99.87 0.1856 0.1828 0.1913 0.2349 0.2331 RANDOM 43.538
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] 1.18 -0.53 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_4_deg 19.841 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_1_deg 6.041 r_angle_refined_deg 1.625 r_angle_other_deg 0.95 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_4_deg 19.841 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_1_deg 6.041 r_angle_refined_deg 1.625 r_angle_other_deg 0.95 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2716 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 71
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing