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The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCB 1VCB and 2OUO experimental model PDB 2OUO 1VCB and 2OUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 PEG 8000, Sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.86 68.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.306 α = 90 b = 102.306 β = 90 c = 144.329 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 PIXEL DECTRIS PILATUS 6M-F 2015-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.7 48.21 99.7 0.079 0.998 14.7 4.2 46323 47.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.79 99.3 0.66 0.571 2.1 3.7
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 1VCB and 2OUO 2.7 48.21 44157 2135 99.67 0.2067 0.2055 0.2088 0.2307 0.2349 RANDOM 62.348
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] -0.05 -0.02 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_3_deg 12.315 r_mcangle_it 6.619 r_dihedral_angle_1_deg 5.251 r_mcbond_it 4.375 r_mcbond_other 4.359 r_angle_refined_deg 1.144 r_angle_other_deg 0.84 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_3_deg 12.315 r_mcangle_it 6.619 r_dihedral_angle_1_deg 5.251 r_mcbond_it 4.375 r_mcbond_other 4.359 r_angle_refined_deg 1.144 r_angle_other_deg 0.84 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7185 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 138
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction