7R05

ATAD2 in complex with PepLite-Ile


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 = 79.539α = 90
b = 79.539β = 90
c = 138.471γ = 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
11.5361.671000.1450.1520.0440.99811.621.639838
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)
11.531.569.93610.4743.30.3319.1

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-VALUE3DAI1.5361.6739764195299.960.1920.19070.215635.161
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]
0.6460.3230.646-2.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_dihedral_angle_4_deg16.171
r_dihedral_angle_3_deg15.993
r_lrange_other11.63
r_lrange_it11.607
r_scangle_it8.516
r_scangle_other8.512
r_scbond_it5.79
r_scbond_other5.264
r_dihedral_angle_1_deg4.987
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_dihedral_angle_4_deg16.171
r_dihedral_angle_3_deg15.993
r_lrange_other11.63
r_lrange_it11.607
r_scangle_it8.516
r_scangle_other8.512
r_scbond_it5.79
r_scbond_other5.264
r_dihedral_angle_1_deg4.987
r_mcangle_it4.125
r_mcangle_other4.124
r_mcbond_other2.905
r_mcbond_it2.901
r_angle_refined_deg1.836
r_angle_other_deg1.489
r_symmetry_nbd_refined0.282
r_symmetry_xyhbond_nbd_refined0.253
r_xyhbond_nbd_refined0.239
r_nbd_other0.236
r_nbd_refined0.223
r_symmetry_nbd_other0.18
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.099
r_chiral_restr0.098
r_symmetry_nbtor_other0.08
r_xyhbond_nbd_other0.015
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing