7QU7

ATAD2 in complex with FragLite16


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 Properties
Matthews coefficientSolvent content
3.9769.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.783α = 90
b = 78.783β = 90
c = 137.078γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.898DiamondI04

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
12.1368.3211000.1940.1980.043117.638.914759
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)
12.132.196.5846.7391.4350.36541

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-VALUE3DAI2.1368.3211470673899.9660.2210.21830.280659.121
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]
-1.073-0.537-1.0733.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.048
r_dihedral_angle_4_deg19.885
r_dihedral_angle_3_deg16.717
r_lrange_it12.319
r_lrange_other12.315
r_scangle_other9.446
r_scangle_it9.445
r_mcangle_it6.47
r_mcangle_other6.468
r_scbond_it6.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.048
r_dihedral_angle_4_deg19.885
r_dihedral_angle_3_deg16.717
r_lrange_it12.319
r_lrange_other12.315
r_scangle_other9.446
r_scangle_it9.445
r_mcangle_it6.47
r_mcangle_other6.468
r_scbond_it6.381
r_scbond_other6.378
r_dihedral_angle_1_deg6.169
r_mcbond_it4.585
r_mcbond_other4.561
r_angle_refined_deg1.556
r_angle_other_deg1.367
r_nbd_other0.285
r_symmetry_nbd_refined0.247
r_xyhbond_nbd_refined0.226
r_symmetry_xyhbond_nbd_refined0.223
r_nbd_refined0.216
r_symmetry_nbd_other0.186
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_other0.102
r_symmetry_nbtor_other0.081
r_chiral_restr0.072
r_xyhbond_nbd_other0.064
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms57
Heterogen Atoms38

Software

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