4QSW

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 5-methyl uridine


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
4.0969.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.59α = 90
b = 79.59β = 90
c = 138.421γ = 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
11.834.5998.30.0816.29.3241862416127.8
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)
11.81.996.50.7982.69.43381

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: 3DAI1.830.9322416122926123597.750.2070.170830.168950.20494RANDOM31.416
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]
-0.12-0.12-0.120.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.872
r_dihedral_angle_3_deg12.903
r_dihedral_angle_4_deg12.527
r_long_range_B_refined9.424
r_long_range_B_other9.422
r_dihedral_angle_1_deg4.757
r_scangle_other4.144
r_mcangle_other2.727
r_mcangle_it2.723
r_scbond_it2.648
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.872
r_dihedral_angle_3_deg12.903
r_dihedral_angle_4_deg12.527
r_long_range_B_refined9.424
r_long_range_B_other9.422
r_dihedral_angle_1_deg4.757
r_scangle_other4.144
r_mcangle_other2.727
r_mcangle_it2.723
r_scbond_it2.648
r_scbond_other2.635
r_mcbond_it1.749
r_mcbond_other1.708
r_angle_refined_deg1.627
r_angle_other_deg0.942
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms43

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling