8XXE | pdb_00008xxe

TtCS-intermediate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldA0A0S3QTD0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.150.1M BIS-TRIS pH 6.5, 2.4M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.91α = 90
b = 109.91β = 90
c = 265.09γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.9792SSRFBL10U2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.0834.461000.1810.1890.99919.325.798252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.131.3130.3630.896

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0834.4693238490099.960.173260.170980.18090.216720.2253RANDOM39.132
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.966
r_long_range_B_other8.058
r_long_range_B_refined8.057
r_dihedral_angle_2_deg7.435
r_scangle_other7.018
r_dihedral_angle_1_deg6.312
r_scbond_it4.766
r_scbond_other4.766
r_mcangle_it4.448
r_mcangle_other4.448
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.966
r_long_range_B_other8.058
r_long_range_B_refined8.057
r_dihedral_angle_2_deg7.435
r_scangle_other7.018
r_dihedral_angle_1_deg6.312
r_scbond_it4.766
r_scbond_other4.766
r_mcangle_it4.448
r_mcangle_other4.448
r_mcbond_it3.447
r_mcbond_other3.447
r_angle_refined_deg1.555
r_angle_other_deg0.48
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10694
Nucleic Acid Atoms
Solvent Atoms598
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing