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PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N11396a in complex with MAP kinase p38-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SO1 PDB entry 6SO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 291 27.5% PEG3350, 0.1 M Bis-Tris propane, pH 6.9, 50 mM ammonium sulfate, 0.2 M 1:1 magnesium chloride:magnesium sulfate,
10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.07 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.91 α = 90 b = 86.614 β = 90 c = 127.537 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 2016-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.73 127.54 98.8 0.113 0.123 0.049 0.991 7.1 6.5 53273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.77 98.9 1.517 1.649 0.638 0.485 6.5 3898
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 6SO1 1.73 71.65 49378 2578 96.2 0.2206 0.2191 0.2486 0.2492 RANDOM 26.922
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] 0.45 -0.36 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 16.354 r_dihedral_angle_1_deg 6.775 r_mcangle_it 3.615 r_mcbond_other 1.956 r_mcbond_it 1.941 r_angle_refined_deg 1.537 r_angle_other_deg 1.529 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 16.354 r_dihedral_angle_1_deg 6.775 r_mcangle_it 3.615 r_mcbond_other 1.956 r_mcbond_it 1.941 r_angle_refined_deg 1.537 r_angle_other_deg 1.529 r_chiral_restr 0.07 r_bond_other_d 0.016 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2746 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing