8B5G

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-3-methyl-1,3-dihydro-2H-benzo[d]azepin-2-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn house

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.906α = 90
b = 52.421β = 90
c = 32.086γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002014-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.61971.3996.30.01352.12.515360
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6191.71850.03122.21.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEIn house1.61921.8081524875894.9380.150.14830.182713.384
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]
0.094-0.051-0.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.061
r_dihedral_angle_4_deg18.736
r_dihedral_angle_3_deg11.322
r_lrange_it5.005
r_lrange_other5.003
r_dihedral_angle_1_deg4.939
r_scangle_it1.663
r_scangle_other1.662
r_angle_other_deg1.35
r_angle_refined_deg1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.061
r_dihedral_angle_4_deg18.736
r_dihedral_angle_3_deg11.322
r_lrange_it5.005
r_lrange_other5.003
r_dihedral_angle_1_deg4.939
r_scangle_it1.663
r_scangle_other1.662
r_angle_other_deg1.35
r_angle_refined_deg1.23
r_mcangle_other1.213
r_mcangle_it1.211
r_scbond_it0.985
r_scbond_other0.985
r_mcbond_it0.694
r_mcbond_other0.668
r_nbd_refined0.206
r_nbtor_refined0.173
r_symmetry_nbd_other0.166
r_symmetry_nbd_refined0.147
r_nbd_other0.13
r_xyhbond_nbd_refined0.107
r_symmetry_xyhbond_nbd_refined0.095
r_symmetry_nbtor_other0.078
r_chiral_restr0.068
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms915
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling