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Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OCL PDB ENTRY 4OCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROPS 6 291 50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.042 α = 90 b = 80.042 β = 90 c = 386.205 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00000 ESRF ID23-1
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 2.249 48.276 99.8 0.058 0.058 20.3 7.8 61223 61223 -100 -100 56.699
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 2.249 2.37 99.2 0.806 0.806 1 8 8721
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 ENTRY 4OCL 2.25 30 61002 61002 3108 99.68 0.2346 0.2346 0.2321 0.226 0.2811 0.2709 RANDOM 54.6609
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] 1.97 1.97 -3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_4_deg 21.474 r_dihedral_angle_3_deg 17.167 r_dihedral_angle_1_deg 6.083 r_scangle_it 2.306 r_scbond_it 1.445 r_angle_refined_deg 1.178 r_mcangle_it 1.064 r_mcbond_it 0.563 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_4_deg 21.474 r_dihedral_angle_3_deg 17.167 r_dihedral_angle_1_deg 6.083 r_scangle_it 2.306 r_scbond_it 1.445 r_angle_refined_deg 1.178 r_mcangle_it 1.064 r_mcbond_it 0.563 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7206 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction