7QYK

ATAD2 in complex with FragLite18


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.009α = 90
b = 79.009β = 90
c = 137.016γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.915DiamondI04-1

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
11.4368.511000.0660.0690.02120.320.747455
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)
11.431.452.8453.010.9770.39818

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-VALUE3DAI1.4361.2947376233699.9560.1960.19560.212429.761
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]
0.1230.0610.123-0.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.575
r_dihedral_angle_4_deg18.881
r_dihedral_angle_3_deg14.467
r_lrange_it10.542
r_lrange_other10.539
r_scangle_it7.146
r_scangle_other7.142
r_dihedral_angle_1_deg4.995
r_scbond_it4.855
r_scbond_other4.853
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.575
r_dihedral_angle_4_deg18.881
r_dihedral_angle_3_deg14.467
r_lrange_it10.542
r_lrange_other10.539
r_scangle_it7.146
r_scangle_other7.142
r_dihedral_angle_1_deg4.995
r_scbond_it4.855
r_scbond_other4.853
r_mcangle_it3.738
r_mcangle_other3.735
r_mcbond_other2.673
r_mcbond_it2.671
r_angle_refined_deg2.196
r_angle_other_deg1.549
r_symmetry_nbd_refined0.35
r_nbd_other0.259
r_nbd_refined0.252
r_xyhbond_nbd_refined0.25
r_symmetry_xyhbond_nbd_refined0.218
r_symmetry_nbd_other0.192
r_nbtor_refined0.188
r_chiral_restr0.113
r_xyhbond_nbd_other0.09
r_symmetry_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms64

Software

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