8PX2

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,3-dimethyl-5-(1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2745.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.949α = 90
b = 52.631β = 90
c = 32.159γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002014-09-12MSINGLE 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
11.6271.9596.70.02426.62.715520
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)
11.621.7183.60.175.61.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.62227.4421542976595.9220.1530.15170.176915.117
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]
0.053-0.002-0.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.908
r_dihedral_angle_3_deg13.468
r_lrange_it6.7
r_lrange_other6.7
r_dihedral_angle_1_deg4.972
r_dihedral_angle_2_deg3.47
r_scangle_it2.809
r_scangle_other2.807
r_scbond_other1.71
r_scbond_it1.708
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.908
r_dihedral_angle_3_deg13.468
r_lrange_it6.7
r_lrange_other6.7
r_dihedral_angle_1_deg4.972
r_dihedral_angle_2_deg3.47
r_scangle_it2.809
r_scangle_other2.807
r_scbond_other1.71
r_scbond_it1.708
r_mcangle_it1.653
r_mcangle_other1.653
r_angle_refined_deg1.044
r_mcbond_it1.012
r_mcbond_other0.978
r_angle_other_deg0.4
r_nbd_refined0.22
r_symmetry_nbd_refined0.216
r_nbtor_refined0.187
r_symmetry_nbd_other0.176
r_nbd_other0.155
r_xyhbond_nbd_refined0.145
r_symmetry_xyhbond_nbd_refined0.099
r_symmetry_nbtor_other0.07
r_chiral_restr0.06
r_gen_planes_refined0.005
r_bond_refined_d0.003
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 Atoms255
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling