4YYN

Crystal structure of TAF1 BD2 Bromodomain bound to a crotonyllysine peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EQFPDB entry 1EQF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M calcium acetate, 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3146.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.009α = 90
b = 66.001β = 90
c = 80.302γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2013-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
11.855099.90.06211.96.127577
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)
11.851.921000.8336.12692

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 1EQF1.8534.326139138399.780.21410.21250.2433RANDOM38.463
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.744
r_dihedral_angle_4_deg21.867
r_dihedral_angle_3_deg16.337
r_dihedral_angle_1_deg6.326
r_angle_refined_deg1.99
r_chiral_restr0.135
r_bond_refined_d0.02
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2182
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction