7PX5

ATAD2 in complex with 1-Methyl-2-quinolone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
4.0869.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.507α = 90
b = 79.507β = 90
c = 138.224γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2014-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54190

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1838.32295.20.0590.0810.0540.9978.42.413347
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1838.2995.20.0160.0220.0150.9992.2

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3DAI2.1838.3221333566594.3870.2080.20640.246132.33
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]
0.0420.0210.042-0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.554
r_dihedral_angle_4_deg18.563
r_dihedral_angle_3_deg18.251
r_lrange_it8.245
r_scangle_it6.529
r_dihedral_angle_1_deg5.841
r_scbond_it4.348
r_mcangle_it3.53
r_mcbond_it2.491
r_angle_refined_deg1.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.554
r_dihedral_angle_4_deg18.563
r_dihedral_angle_3_deg18.251
r_lrange_it8.245
r_scangle_it6.529
r_dihedral_angle_1_deg5.841
r_scbond_it4.348
r_mcangle_it3.53
r_mcbond_it2.491
r_angle_refined_deg1.769
r_nbtor_refined0.327
r_symmetry_nbd_refined0.282
r_nbd_refined0.232
r_xyhbond_nbd_refined0.185
r_symmetry_xyhbond_nbd_refined0.181
r_chiral_restr0.118
r_bond_refined_d0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1069
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing