6FDK

Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B5Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.1 M MES pH 6.5, 12% PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.0539.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.815α = 90
b = 56.937β = 104.86
c = 60.695γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.980ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.646.2298.860.071780.027390.99917.066.74132623.74
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.65799.90.64740.5611.327

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5B5Q1.646.2239198202198.880.171220.169550.20333RANDOM23.148
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]
-0.120.35-0.190.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.692
r_dihedral_angle_3_deg14.169
r_dihedral_angle_4_deg14.026
r_long_range_B_refined6.377
r_long_range_B_other6.376
r_dihedral_angle_1_deg6.224
r_scangle_other4.544
r_scbond_it3.047
r_scbond_other3.046
r_angle_refined_deg2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.692
r_dihedral_angle_3_deg14.169
r_dihedral_angle_4_deg14.026
r_long_range_B_refined6.377
r_long_range_B_other6.376
r_dihedral_angle_1_deg6.224
r_scangle_other4.544
r_scbond_it3.047
r_scbond_other3.046
r_angle_refined_deg2.53
r_mcangle_it2.301
r_mcangle_other2.3
r_mcbond_it1.64
r_mcbond_other1.638
r_angle_other_deg1.287
r_chiral_restr0.19
r_bond_refined_d0.03
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2543
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing