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Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib
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, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.401 α = 90 b = 44.97 β = 98.4 c = 200.043 γ = 90
Symmetry Space Group P 1 2 1
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 1.99 197.898 96.8 0.078 0.078 9.1 3.2 74800 74800 -100 -100 32.52
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 1.99 2.1 88 0.6 0.6 1.3 3.2 9816
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 1.99 30 74685 74685 3757 96.48 0.2181 0.2181 0.2158 0.2141 0.2623 0.2606 RANDOM 40.609
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] -1.19 0.06 0.66 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_4_deg 18.896 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 7.486 r_scangle_it 6.464 r_scbond_it 4.329 r_mcangle_it 2.613 r_angle_refined_deg 1.933 r_mcbond_it 1.509 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_4_deg 18.896 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 7.486 r_scangle_it 6.464 r_scbond_it 4.329 r_mcangle_it 2.613 r_angle_refined_deg 1.933 r_mcbond_it 1.509 r_chiral_restr 0.156 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7299 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 3
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction