7OET

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxo-1-(tetrahydro-2H-pyran-4-yl)ethyl)-6-oxo-N-(2-phenyl-2-(pyridin-2-yl)ethyl)-1,6-dihydropyridine-3-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2344.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.62α = 90
b = 52.39β = 90
c = 31.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.96600ESRFID30B

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
11.4142.2999.30.0370.99917.44.323909
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)
11.411.4399.60.6560.7182.14.5

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 structure1.4115.69623731120499.2260.1810.180.195928.07
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]
-0.8240.1770.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.036
r_dihedral_angle_4_deg16.238
r_dihedral_angle_3_deg11.743
r_lrange_it5.622
r_lrange_other5.579
r_dihedral_angle_1_deg4.625
r_scangle_it3.807
r_scangle_other3.805
r_mcangle_it2.579
r_mcangle_other2.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.036
r_dihedral_angle_4_deg16.238
r_dihedral_angle_3_deg11.743
r_lrange_it5.622
r_lrange_other5.579
r_dihedral_angle_1_deg4.625
r_scangle_it3.807
r_scangle_other3.805
r_mcangle_it2.579
r_mcangle_other2.577
r_scbond_it2.305
r_scbond_other2.303
r_mcbond_it1.578
r_mcbond_other1.564
r_angle_other_deg1.254
r_angle_refined_deg1.128
r_nbd_refined0.195
r_nbtor_refined0.171
r_symmetry_nbd_other0.165
r_symmetry_nbd_refined0.152
r_nbd_other0.137
r_xyhbond_nbd_refined0.109
r_symmetry_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.081
r_chiral_restr0.063
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 Atoms921
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling