4IR3

Crystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-amino-1-(pyrimidin-2-yl)indolizin-3-yl]ethanone (GSK2833282A)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277.1518% PEG 1000, 17% glycerol, 0.1M HEPES pH 7.0 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.1970.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.1α = 90
b = 96.42β = 90
c = 57.71γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-09-23MSINGLE 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
1229.511000.088115158601584733.5
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)
122.111000.6732.252283

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 3G0L227.482158471505779099.950.211260.209530.2455RANDOM39.986
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]
1.88-0.82-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.492
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg13.311
r_dihedral_angle_1_deg6.262
r_angle_refined_deg1.593
r_angle_other_deg0.785
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.492
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg13.311
r_dihedral_angle_1_deg6.262
r_angle_refined_deg1.593
r_angle_other_deg0.785
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms937
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms43

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling