2DVR

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherBD1 NATIVE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, CO-CRYSTALLIZAATION6.5298PEGMME 5K, AS, pH 6.50, VAPOR DIFFUSION, CO-CRYSTALLIZAATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.533α = 90
b = 55.238β = 93.92
c = 67.735γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC2004-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B2SPring-8BL44B2

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
12.045098.40.0623.626362-3
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)
2.042.1188.80.3313

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 REPLACEMENTTHROUGHOUTBD1 NATIVE2.3201775996599.80.1820.180.243RANDOM34.63
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]
0.67-1.3-0.35-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.851
r_scangle_it4.467
r_scbond_it2.982
r_mcangle_it1.736
r_angle_refined_deg1.691
r_mcbond_it0.918
r_symmetry_hbond_refined0.414
r_symmetry_vdw_refined0.27
r_nbd_refined0.251
r_xyhbond_nbd_refined0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.851
r_scangle_it4.467
r_scbond_it2.982
r_mcangle_it1.736
r_angle_refined_deg1.691
r_mcbond_it0.918
r_symmetry_hbond_refined0.414
r_symmetry_vdw_refined0.27
r_nbd_refined0.251
r_xyhbond_nbd_refined0.181
r_chiral_restr0.116
r_bond_refined_d0.022
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2887
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms

Software

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