7R00

ATAD2 in complex with FragLite33


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 = 79.331α = 90
b = 79.331β = 90
c = 137.081γ = 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
11.48137.081000.0720.0760.0230.9991615.943256
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)
11.481.511.8242.211.2250.4375.6

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-VALUE3DAI1.4861.49643179213199.9210.2080.20670.236732.147
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]
-0.787-0.393-0.7872.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_dihedral_angle_4_deg17.006
r_dihedral_angle_3_deg14.272
r_lrange_it9.94
r_lrange_other9.937
r_scangle_other7.374
r_scangle_it7.356
r_scbond_it4.879
r_scbond_other4.86
r_dihedral_angle_1_deg4.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_dihedral_angle_4_deg17.006
r_dihedral_angle_3_deg14.272
r_lrange_it9.94
r_lrange_other9.937
r_scangle_other7.374
r_scangle_it7.356
r_scbond_it4.879
r_scbond_other4.86
r_dihedral_angle_1_deg4.712
r_mcangle_it3.737
r_mcangle_other3.735
r_mcbond_other2.745
r_mcbond_it2.744
r_angle_refined_deg1.821
r_angle_other_deg1.505
r_symmetry_xyhbond_nbd_refined0.27
r_xyhbond_nbd_refined0.252
r_nbd_refined0.23
r_nbd_other0.212
r_symmetry_nbd_other0.19
r_symmetry_nbd_refined0.18
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_other0.097
r_chiral_restr0.091
r_symmetry_nbtor_other0.083
r_xyhbond_nbd_other0.039
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing