4QSU

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with thymine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5277.15apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.0469.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.12α = 90
b = 79.12β = 90
c = 138.06γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2013-05-10MSINGLE 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
11.934.511000.09812.77.3209042084227.5
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)
11.921000.8542.27.32976

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb id: 3DAI1.934.3322084219771107099.950.2060.168970.16710.20342RANDOM31.704
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]
-0.16-0.16-0.160.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.949
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg13.378
r_long_range_B_refined8.951
r_long_range_B_other8.949
r_scangle_other4.609
r_dihedral_angle_1_deg4.517
r_scbond_it2.92
r_scbond_other2.912
r_mcangle_other2.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.949
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg13.378
r_long_range_B_refined8.951
r_long_range_B_other8.949
r_scangle_other4.609
r_dihedral_angle_1_deg4.517
r_scbond_it2.92
r_scbond_other2.912
r_mcangle_other2.449
r_mcangle_it2.446
r_angle_refined_deg1.65
r_mcbond_it1.619
r_mcbond_other1.606
r_angle_other_deg0.857
r_chiral_restr0.112
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms47

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling