4QUU

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5


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
3.7367.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.201α = 90
b = 79.201β = 90
c = 139.141γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2012-11-14MSINGLE 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
11.834.441000.0916.29.7245882452726.1
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)
11.81.91000.8942.49.93483

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: 3DAI1.834.4222452723271125599.860.2020.170370.168810.2004RANDOM29.089
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]
0.020.020.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_dihedral_angle_4_deg19.111
r_dihedral_angle_3_deg12.526
r_long_range_B_other9.738
r_long_range_B_refined9.737
r_dihedral_angle_1_deg4.424
r_scangle_other3.5
r_scbond_it2.349
r_scbond_other2.335
r_mcangle_other1.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_dihedral_angle_4_deg19.111
r_dihedral_angle_3_deg12.526
r_long_range_B_other9.738
r_long_range_B_refined9.737
r_dihedral_angle_1_deg4.424
r_scangle_other3.5
r_scbond_it2.349
r_scbond_other2.335
r_mcangle_other1.841
r_mcangle_it1.833
r_angle_refined_deg1.528
r_mcbond_it1.218
r_mcbond_other1.209
r_angle_other_deg0.82
r_chiral_restr0.099
r_bond_refined_d0.016
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 Atoms1119
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms41

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling