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The structure of polycomb ULD complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HPM PDB ENTRY 4HPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100MM MES, PH 6.5, 50MM MGCL2, 7% ISOPROPANOL, 6% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.95 58.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.275 α = 90 b = 78.275 β = 90 c = 43.119 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2014-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 99.8 0.09 33.93 10 5292 2
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 2.54 99.6 0.48 3.27 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4HPM 2.51 39.14 5015 267 99.74 0.23748 0.23253 0.2357 0.32833 0.328 RANDOM 56.18
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] 0.54 0.27 0.54 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 35.066 r_dihedral_angle_2_deg 30.727 r_dihedral_angle_3_deg 19.007 r_scangle_it 13.878 r_mcangle_it 10.749 r_scbond_it 10.726 r_mcbond_it 8.324 r_mcbond_other 8.319 r_dihedral_angle_1_deg 6.121 r_angle_refined_deg 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 35.066 r_dihedral_angle_2_deg 30.727 r_dihedral_angle_3_deg 19.007 r_scangle_it 13.878 r_mcangle_it 10.749 r_scbond_it 10.726 r_mcbond_it 8.324 r_mcbond_other 8.319 r_dihedral_angle_1_deg 6.121 r_angle_refined_deg 1.783 r_angle_other_deg 1.144 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 692 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing