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BRD4 in complex with ERK5 inhibitor XMD8-92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 BRD4 10mg/ml
30w/v Jeffamine ED-2001
0.1M HEPES pH7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.923 α = 90 b = 53.923 β = 90 c = 89.32 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS3 S 6M 2016-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.969 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 1.7 46.7 100 0.081 1 14.4 10.3 17138
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 1.7 1.73 100 0.96 0.91 2.3 10.4
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 2OSS 1.7 46.7 16240 862 99.99 0.1891 0.18667 0.1954 0.23267 0.2312 RANDOM 29.126
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] -1.54 -0.77 -1.54 4.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.45 r_dihedral_angle_4_deg 21.004 r_dihedral_angle_3_deg 12.344 r_long_range_B_refined 7.656 r_long_range_B_other 7.641 r_dihedral_angle_1_deg 7.078 r_scangle_other 5.514 r_mcangle_it 4.121 r_mcangle_other 4.118 r_scbond_it 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.45 r_dihedral_angle_4_deg 21.004 r_dihedral_angle_3_deg 12.344 r_long_range_B_refined 7.656 r_long_range_B_other 7.641 r_dihedral_angle_1_deg 7.078 r_scangle_other 5.514 r_mcangle_it 4.121 r_mcangle_other 4.118 r_scbond_it 3.47 r_scbond_other 3.467 r_mcbond_it 2.948 r_mcbond_other 2.886 r_angle_refined_deg 1.888 r_angle_other_deg 1.05 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1015 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing