2E3K

Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DVV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.828α = 90
b = 128.591β = 104.7
c = 45.847γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 42005-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
12.35097.70.0483.72295522434-3
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)
2.32.3897.90.1663.7

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 REPLACEMENTTHROUGHOUT2DVV2.32021151114498.030.204470.200960.26757RANDOM43.691
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]
1.781.26-0.85-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.94
r_scangle_it3.728
r_scbond_it2.753
r_mcangle_it2.424
r_angle_refined_deg1.871
r_mcbond_it1.489
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.259
r_nbd_refined0.246
r_xyhbond_nbd_refined0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.94
r_scangle_it3.728
r_scbond_it2.753
r_mcangle_it2.424
r_angle_refined_deg1.871
r_mcbond_it1.489
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.259
r_nbd_refined0.246
r_xyhbond_nbd_refined0.196
r_chiral_restr0.12
r_bond_refined_d0.023
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3766
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing