7OE6

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N4-hydroxycyclohexyl-N2-methyl-5-phenylethyl-furan-2,4-dicarboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29830% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2645.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.007α = 90
b = 52.532β = 90
c = 32.14γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002019-01-22MSINGLE 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)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
11.7642.4497.50.0790.99711.53.412247
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)
11.761.8699.60.4670.8092.73.3

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 DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEin house structure1.76232.141220561796.7880.1580.15610.189320.143
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]
-0.192-0.5410.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.218
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg12.477
r_lrange_it7.286
r_lrange_other6.308
r_dihedral_angle_1_deg5.184
r_scangle_it3.106
r_scangle_other3.104
r_mcangle_other2.476
r_mcangle_it2.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.218
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg12.477
r_lrange_it7.286
r_lrange_other6.308
r_dihedral_angle_1_deg5.184
r_scangle_it3.106
r_scangle_other3.104
r_mcangle_other2.476
r_mcangle_it2.471
r_scbond_it1.833
r_scbond_other1.831
r_mcbond_it1.418
r_mcbond_other1.384
r_angle_other_deg1.226
r_angle_refined_deg1.187
r_nbd_refined0.189
r_nbd_other0.177
r_symmetry_nbd_other0.167
r_xyhbond_nbd_refined0.165
r_nbtor_refined0.163
r_symmetry_nbd_refined0.148
r_symmetry_xyhbond_nbd_refined0.119
r_symmetry_nbtor_other0.079
r_chiral_restr0.064
r_symmetry_xyhbond_nbd_other0.028
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms919
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling