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Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 20 mM Tris, 500 mM NaCl, 1 mM EDTA, 1.5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.514 α = 90 b = 120.514 β = 90 c = 27.209 γ = 120
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 2005-07-16 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.2821, 1.2826, 1.25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 99.1 0.066 15.9 3.7 8143
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.258 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2.5 104.26 8143 7686 373 99.04 0.21137 0.20971 0.208 0.24418 0.2431 RANDOM 42.867
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] 0.65 0.32 0.65 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_3_deg 17.283 r_dihedral_angle_4_deg 13.608 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.985 r_scbond_it 2.251 r_angle_refined_deg 1.319 r_mcangle_it 1.076 r_mcbond_it 0.598 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_3_deg 17.283 r_dihedral_angle_4_deg 13.608 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.985 r_scbond_it 2.251 r_angle_refined_deg 1.319 r_mcangle_it 1.076 r_mcbond_it 0.598 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1589 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction MADNESS data reduction