2YEL

Crystal Structure of the First Bromodomain of Human Brd4 with the inhibitor GW841819X


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSSPDB ENTRY 2OSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.517.5% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS TRIS PH 5.5.
Crystal Properties
Matthews coefficientSolvent content
2.1442.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.083α = 90
b = 44.308β = 90
c = 78.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002009-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRF

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
11.6544.311000.099.56.8516241214.6
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)
11.621.711000.393.76.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OSS1.6544.32154228161000.167570.165270.21119RANDOM22.153
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]
1.22-1.09-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.031
r_dihedral_angle_4_deg15.431
r_dihedral_angle_3_deg11.656
r_dihedral_angle_1_deg5.006
r_scangle_it3.471
r_scbond_it2.14
r_mcangle_it1.762
r_angle_refined_deg1.244
r_mcbond_it0.928
r_angle_other_deg0.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.031
r_dihedral_angle_4_deg15.431
r_dihedral_angle_3_deg11.656
r_dihedral_angle_1_deg5.006
r_scangle_it3.471
r_scbond_it2.14
r_mcangle_it1.762
r_angle_refined_deg1.244
r_mcbond_it0.928
r_angle_other_deg0.847
r_mcbond_other0.169
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1062
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing