2DVS | pdb_00002dvs

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 modelOtherBRD2-BD1 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 = 114.149α = 90
b = 55.248β = 94.12
c = 67.364γ = 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
12.045099.50.0573.626788-3
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)
2.042.1198.90.1883.6

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTBRD2-BD1 NATIVE2.042025421134599.30.1940.1920.231RANDOM31.48
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]
0.64-1.52-0.52-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.566
r_scangle_it4.163
r_scbond_it3.041
r_mcangle_it1.523
r_angle_refined_deg1.413
r_mcbond_it0.812
r_symmetry_hbond_refined0.292
r_symmetry_vdw_refined0.244
r_nbd_refined0.229
r_xyhbond_nbd_refined0.151
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2807
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms

Software

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