8B5J

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-1,3-dimethyl-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 DROP27330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2445.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.802α = 90
b = 52.416β = 90
c = 31.983γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-02-11MSINGLE 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
11.652.4292.60.0160.99847.93.515172
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)
11.61.769.40.0660.957152.6

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 house1.60335.9271512172891.7810.1470.14590.170716.573
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]
0.01-0.2640.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.899
r_dihedral_angle_4_deg22.154
r_dihedral_angle_3_deg10.663
r_lrange_it5.78
r_lrange_other5.778
r_dihedral_angle_1_deg4.635
r_scangle_it2.153
r_scangle_other2.152
r_mcangle_other1.56
r_mcangle_it1.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.899
r_dihedral_angle_4_deg22.154
r_dihedral_angle_3_deg10.663
r_lrange_it5.78
r_lrange_other5.778
r_dihedral_angle_1_deg4.635
r_scangle_it2.153
r_scangle_other2.152
r_mcangle_other1.56
r_mcangle_it1.554
r_angle_other_deg1.324
r_angle_refined_deg1.288
r_scbond_it1.288
r_scbond_other1.287
r_mcbond_it0.901
r_mcbond_other0.849
r_nbd_refined0.205
r_nbtor_refined0.171
r_symmetry_nbd_other0.166
r_nbd_other0.139
r_symmetry_nbd_refined0.125
r_symmetry_xyhbond_nbd_refined0.103
r_xyhbond_nbd_refined0.098
r_symmetry_nbtor_other0.08
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 Atoms931
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling