6YQZ

N-terminal domain of BRD4 with biphenyl-methyamino-dimethylpyridazinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29820%w/v PEG 3350, 0.2M sodium sulphate,0.1M bis-tris-propane (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.1843.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.94α = 90
b = 44.37β = 90
c = 78.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.3939.0398.50.0830.0940.04394.126727
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.391.4795.20.5130.5130.6190.3381.52.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIn house structure1.3939.0325379134898.170.17320.17170.2037RANDOM18.245
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]
1.52-0.44-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.96
r_dihedral_angle_3_deg12.568
r_dihedral_angle_4_deg10.168
r_dihedral_angle_1_deg5.547
r_angle_other_deg1.27
r_angle_refined_deg1.194
r_chiral_restr0.062
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.96
r_dihedral_angle_3_deg12.568
r_dihedral_angle_4_deg10.168
r_dihedral_angle_1_deg5.547
r_angle_other_deg1.27
r_angle_refined_deg1.194
r_chiral_restr0.062
r_gen_planes_refined0.005
r_bond_refined_d0.004
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 Atoms255
Heterogen Atoms27

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction