5D3N

First bromodomain of BRD4 bound to inhibitor XD40


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Tacsimate
Crystal Properties
Matthews coefficientSolvent content
2.2445.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.08α = 90
b = 43.5β = 90
c = 79.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
1243.599.80.0819.549604
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)
122.111000.5122.41368

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1539.55697576499.650.211020.208320.23496RANDOM40.812
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]
3.93-1.74-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.529
r_dihedral_angle_3_deg16.776
r_dihedral_angle_4_deg13.604
r_dihedral_angle_1_deg5.525
r_long_range_B_refined4.21
r_long_range_B_other4.152
r_mcangle_it1.703
r_mcangle_other1.702
r_scangle_other1.641
r_angle_refined_deg1.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.529
r_dihedral_angle_3_deg16.776
r_dihedral_angle_4_deg13.604
r_dihedral_angle_1_deg5.525
r_long_range_B_refined4.21
r_long_range_B_other4.152
r_mcangle_it1.703
r_mcangle_other1.702
r_scangle_other1.641
r_angle_refined_deg1.322
r_mcbond_it1.111
r_mcbond_other1.105
r_scbond_it1.061
r_scbond_other1.06
r_angle_other_deg0.789
r_chiral_restr0.065
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1056
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction