5MGJ

Crystal Structure of BAZ2A bromodomain in complex with 1-methylpyridine derivative 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720% PEG3350, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.5265.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.737α = 90
b = 95.737β = 90
c = 32.96γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.00ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.147.871000.2060.2180.070.9959.29.710377
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.161001.0740.78510.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4LZ22.131.3371.341035956899.940.19360.19190.222435.9747
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.959
f_angle_d1.009
f_chiral_restr0.035
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms853
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms14

Software

Software
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing