7QUM

ATAD2 in complex with FragLite2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.163α = 90
b = 79.163β = 90
c = 138.226γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.976DiamondI04-1

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
11.561.4296.80.0770.0810.0240.99918.219.940300
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)
11.51.533.2673.5151.260.37112.6

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-VALUE3DAI1.561.4240253205796.5250.1990.19730.223332.315
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]
0.040.020.04-0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_3_deg13.987
r_dihedral_angle_4_deg13.562
r_lrange_other11.668
r_lrange_it11.629
r_scangle_other7.577
r_scangle_it7.559
r_scbond_it5.244
r_scbond_other5.241
r_dihedral_angle_1_deg4.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_3_deg13.987
r_dihedral_angle_4_deg13.562
r_lrange_other11.668
r_lrange_it11.629
r_scangle_other7.577
r_scangle_it7.559
r_scbond_it5.244
r_scbond_other5.241
r_dihedral_angle_1_deg4.61
r_mcangle_it4.203
r_mcangle_other4.2
r_mcbond_it2.955
r_mcbond_other2.952
r_angle_refined_deg1.993
r_angle_other_deg1.527
r_symmetry_nbd_refined0.535
r_nbd_refined0.515
r_xyhbond_nbd_refined0.38
r_nbd_other0.355
r_symmetry_nbd_other0.292
r_symmetry_xyhbond_nbd_refined0.26
r_symmetry_xyhbond_nbd_other0.222
r_nbtor_refined0.178
r_chiral_restr0.102
r_symmetry_nbtor_other0.083
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_xyhbond_nbd_other0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
xia2data scaling
PHASERphasing