☰ Navigation Tabs
Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X1P PDB ENTRIES 2X1P AND 2O95 experimental model PDB 2O95 PDB ENTRIES 2X1P AND 2O95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROPS 6 291 50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.258 α = 100.08 b = 63.431 β = 92.75 c = 100.111 γ = 90.62
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 PSI PILATUS 6M 2013-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00753 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.392 98.44 96.4 0.081 0.081 10.1 3.5 41691 41691 -100 -100 54.346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.392 2.52 90.4 0.634 0.634 1.2 3.4 5720
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRIES 2X1P AND 2O95 2.4 30 41609 41609 2089 97.21 0.198 0.198 0.1951 0.1901 0.2522 0.2445 RANDOM 47.387
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] 2.23 0.26 0.56 -1.53 -0.5 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 23.462 r_dihedral_angle_3_deg 18.967 r_dihedral_angle_1_deg 7.195 r_scangle_it 4.286 r_scbond_it 2.713 r_angle_refined_deg 1.733 r_mcangle_it 1.719 r_mcbond_it 0.888 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 23.462 r_dihedral_angle_3_deg 18.967 r_dihedral_angle_1_deg 7.195 r_scangle_it 4.286 r_scbond_it 2.713 r_angle_refined_deg 1.733 r_mcangle_it 1.719 r_mcbond_it 0.888 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7263 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction