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Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RPG polyalanine models of PDB entries 3RPG and 3LZ0 experimental model PDB 3LZ0 polyalanine models of PDB entries 3RPG and 3LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Modified micro batch under oil 7.5 294 25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.12 60.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.923 α = 90 b = 180.049 β = 90 c = 375.251 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 2013-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2846 45 99.4 0.063 16.5 3.9 54219 54142 -4 105.01
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 3.2846 3.46 99.8 0.64 0.64 1.2 3.9 7877
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 polyalanine models of PDB entries 3RPG and 3LZ0 3.2846 45 1.34 54142 54119 2750 99.1 0.1993 0.1993 0.197 0.2003 0.2452 0.2487 random 137.4911
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.715 f_angle_d 0.504 f_chiral_restr 0.02 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11201 Nucleic Acid Atoms 5925 Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction