3DAI

Crystal structure of the bromodomain of the human ATAD2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSSPDB entry 2OSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52772M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0769.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.616α = 90
b = 79.616β = 90
c = 137.55γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9539.8199.90.0850.08520.510.819492
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0699.70.7790.7792.99.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 entry 2OSS1.9539.8119461100099.860.2030.2030.2010.24RANDOM23.193
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]
0.230.120.23-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.626
r_dihedral_angle_4_deg21.22
r_dihedral_angle_3_deg15.034
r_scangle_it9.649
r_scbond_it7.377
r_dihedral_angle_1_deg4.803
r_mcangle_it4.798
r_mcbond_it3.394
r_angle_refined_deg1.316
r_angle_other_deg1.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.626
r_dihedral_angle_4_deg21.22
r_dihedral_angle_3_deg15.034
r_scangle_it9.649
r_scbond_it7.377
r_dihedral_angle_1_deg4.803
r_mcangle_it4.798
r_mcbond_it3.394
r_angle_refined_deg1.316
r_angle_other_deg1.052
r_mcbond_other1.02
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1064
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms11

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction