4XY8

Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HME 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.716α = 90
b = 43.604β = 104.34
c = 40.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2013-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.52

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.719.55997.70.0860.0860.090.02920.39.61484114841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7995.20.3370.3370.1157.49.42064

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 REPLACEMENTTHROUGHOUT3HME1.719.541408674897.190.15020.14820.1857RANDOM15.873
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]
-0.23-0.570.030.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg15.703
r_dihedral_angle_3_deg13.848
r_dihedral_angle_1_deg4.559
r_mcangle_it3.36
r_mcbond_other2.558
r_mcbond_it2.557
r_angle_refined_deg1.747
r_angle_other_deg0.828
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg15.703
r_dihedral_angle_3_deg13.848
r_dihedral_angle_1_deg4.559
r_mcangle_it3.36
r_mcbond_other2.558
r_mcbond_it2.557
r_angle_refined_deg1.747
r_angle_other_deg0.828
r_chiral_restr0.093
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 Atoms920
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms20

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction