9X7C | pdb_00009x7c

Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Mivebresib ABBV-075


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SB6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981M Hepes (7.5), 26% PEG 3350, 0.2M Amm sulphate
Crystal Properties
Matthews coefficientSolvent content
2.8456.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.7α = 90
b = 55.96β = 95.53
c = 69.33γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker AXIOM 2002025-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5678

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.356.5999.90.0970.9729.33.119465
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)RedundancyNumber Unique Reflections (All)
12.32.390.2610.545

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.356.591851794799.90.215130.211570.22130.284030.27RANDOM19.815
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]
-0.1-0.07-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.429
r_long_range_B_refined13.371
r_long_range_B_other13.37
r_dihedral_angle_2_deg8.079
r_dihedral_angle_1_deg6.627
r_scangle_other3.674
r_mcangle_it2.786
r_angle_other_deg2.307
r_scbond_it2.251
r_scbond_other2.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.429
r_long_range_B_refined13.371
r_long_range_B_other13.37
r_dihedral_angle_2_deg8.079
r_dihedral_angle_1_deg6.627
r_scangle_other3.674
r_mcangle_it2.786
r_angle_other_deg2.307
r_scbond_it2.251
r_scbond_other2.251
r_angle_refined_deg1.738
r_mcbond_it1.703
r_chiral_restr0.12
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_4_deg
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_mcbond_other
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2685
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing