7QZZ

ATAD2 in complex with FragLite31


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 Properties
Matthews coefficientSolvent content
4.0469.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.257α = 90
b = 79.257β = 90
c = 137.706γ = 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 I04-10.898DiamondI04-1

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
12.5268.851000.70.7170.1560.95910.737.89241
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.522.6211.2982.4440.46338.8

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-VALUE3DAI2.5268.73391964341000.2050.20310.239962.564
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]
-1.145-0.572-1.1453.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.769
r_dihedral_angle_3_deg16.57
r_dihedral_angle_4_deg14.339
r_lrange_it13.918
r_scangle_it11.061
r_scbond_it8.08
r_mcangle_it7.216
r_dihedral_angle_1_deg5.454
r_mcbond_it5.048
r_angle_refined_deg1.677
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.769
r_dihedral_angle_3_deg16.57
r_dihedral_angle_4_deg14.339
r_lrange_it13.918
r_scangle_it11.061
r_scbond_it8.08
r_mcangle_it7.216
r_dihedral_angle_1_deg5.454
r_mcbond_it5.048
r_angle_refined_deg1.677
r_nbtor_refined0.329
r_nbd_refined0.251
r_xyhbond_nbd_refined0.243
r_symmetry_nbd_refined0.185
r_symmetry_xyhbond_nbd_refined0.147
r_chiral_restr0.12
r_bond_refined_d0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms45

Software

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