4IR4

Crystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone (GSK2834113A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G0LPDB entry 3G0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.25277.1532% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.25 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.2370.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.699α = 90
b = 96.465β = 90
c = 57.741γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
12.0519.6899.80.127.95147891477430.8
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)
12.052.1699.80.79125.12097

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 3G0L2.0519.62147741402674799.560.185820.183760.2276RANDOM44.822
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]
4.37-1.68-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.876
r_dihedral_angle_4_deg14.07
r_dihedral_angle_3_deg12.742
r_dihedral_angle_1_deg5.764
r_angle_refined_deg1.577
r_angle_other_deg0.882
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.876
r_dihedral_angle_4_deg14.07
r_dihedral_angle_3_deg12.742
r_dihedral_angle_1_deg5.764
r_angle_refined_deg1.577
r_angle_other_deg0.882
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms937
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms56

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling