7R0Y

ATAD2 in complex with PepLite-Glu


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 = 79.288α = 90
b = 79.288β = 90
c = 138.015γ = 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
11.4361.4899.50.0860.0910.0270.99917.319.547816
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)
11.431.452.9433.2521.3530.19510.3

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-VALUE3DAI1.4361.4847744233599.340.1960.19510.213534.361
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]
0.1620.0810.162-0.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.342
r_dihedral_angle_3_deg15.232
r_dihedral_angle_4_deg14.137
r_lrange_it12.973
r_scangle_it9.067
r_scbond_it6.192
r_dihedral_angle_1_deg4.547
r_mcangle_it4.385
r_mcbond_it3.024
r_angle_refined_deg2.633
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.342
r_dihedral_angle_3_deg15.232
r_dihedral_angle_4_deg14.137
r_lrange_it12.973
r_scangle_it9.067
r_scbond_it6.192
r_dihedral_angle_1_deg4.547
r_mcangle_it4.385
r_mcbond_it3.024
r_angle_refined_deg2.633
r_symmetry_nbd_refined0.639
r_symmetry_xyhbond_nbd_refined0.498
r_nbtor_refined0.321
r_xyhbond_nbd_refined0.319
r_nbd_refined0.233
r_chiral_restr0.151
r_bond_refined_d0.019
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing