4TT6

Crystal structure of ATAD2A bromodomain double mutant N1063A-Y1064A in apo form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52782.0M Ammonium sulfate, 0.1M Bis-Tris pH5.5
Crystal Properties
Matthews coefficientSolvent content
4.1370.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.639α = 90
b = 79.639β = 90
c = 138.271γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDADSC QUANTUM 315r2013-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1248.831000.1110.0180.99931.440.718358
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.7130.1120.9788.340.21315

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 REPLACEMENTTHROUGHOUT3DAI248.83182999351000.1650.1650.177RANDOM24.88
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]
-0.04-0.02-0.040.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.576
r_mcbond_it18.294
r_mcbond_other18.204
r_mcangle_it17.53
r_dihedral_angle_4_deg15.454
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg4.571
r_angle_refined_deg1.36
r_angle_other_deg0.843
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.576
r_mcbond_it18.294
r_mcbond_other18.204
r_mcangle_it17.53
r_dihedral_angle_4_deg15.454
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg4.571
r_angle_refined_deg1.36
r_angle_other_deg0.843
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
MAIN-CHAIN ANGLE OTHER ATOMS (A**2)
r_scbond_it
SIDE-CHAIN BOND OTHER ATOMS (A**2)
r_scangle_it
SIDE-CHAIN ANGLE OTHER ATOMS (A**2)
LONG RANGE B REFINED ATOMS (A**2)
LONG RANGE B OTHER ATOMS (A**2)
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1074
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction