6TPY

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 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
othernot published

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M BTP pH8.5, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.694α = 90
b = 43.252β = 90
c = 79.181γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.879.1899.90.99610.56.112890
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.9499.90.7812.76.1

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-VALUEnot published1.839.591284462799.860.2010.19870.254929.2
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]
1.497-0.578-0.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.533
r_dihedral_angle_3_deg13.028
r_dihedral_angle_4_deg10.948
r_lrange_it8.454
r_lrange_other8.454
r_scangle_it6.207
r_scangle_other6.204
r_dihedral_angle_1_deg5.602
r_mcangle_other4.206
r_mcangle_it4.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.533
r_dihedral_angle_3_deg13.028
r_dihedral_angle_4_deg10.948
r_lrange_it8.454
r_lrange_other8.454
r_scangle_it6.207
r_scangle_other6.204
r_dihedral_angle_1_deg5.602
r_mcangle_other4.206
r_mcangle_it4.194
r_scbond_it3.88
r_scbond_other3.877
r_mcbond_it2.826
r_mcbond_other2.789
r_angle_refined_deg1.296
r_angle_other_deg1.185
r_nbd_refined0.195
r_nbd_other0.195
r_xyhbond_nbd_refined0.187
r_symmetry_nbd_other0.174
r_symmetry_xyhbond_nbd_refined0.174
r_nbtor_refined0.173
r_symmetry_nbd_refined0.168
r_symmetry_nbtor_other0.081
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1062
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling