☰ Navigation Tabs
PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13619a 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 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.72 α = 90 b = 87.21 β = 90 c = 125.65 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 2016-02-11 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 1.57 71.64 99.8 0.059 0.064 0.025 0.998 15.4 6.6 70942
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 1.57 1.61 99.7 1.367 1.493 0.592 0.467 6.2 5166
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 6SO1 1.57 71.64 67351 3516 99.73 0.1912 0.1902 0.2167 0.2099 0.2319 RANDOM 28.826
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] 0.53 -0.32 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 18.505 r_dihedral_angle_3_deg 16.435 r_dihedral_angle_1_deg 6.707 r_mcangle_it 3.899 r_mcbond_other 2.408 r_mcbond_it 2.385 r_angle_refined_deg 1.667 r_angle_other_deg 1.628 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 18.505 r_dihedral_angle_3_deg 16.435 r_dihedral_angle_1_deg 6.707 r_mcangle_it 3.899 r_mcbond_other 2.408 r_mcbond_it 2.385 r_angle_refined_deg 1.667 r_angle_other_deg 1.628 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2723 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing