6FDQ | pdb_00006fdq

Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277.15100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane
Crystal Properties
Matthews coefficientSolvent content
2.3247.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.59α = 90
b = 57.037β = 94.73
c = 114.593γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.980ESRFID23-1

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
12.343.4497.560.072890.10310.9943.571.924597
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.38295.660.490.6930.7551.081.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5B5Q2.343.4423430114297.660.231850.229240.230.283970.28RANDOM46.786
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]
2-0.12-1.92-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.956
r_dihedral_angle_3_deg19.235
r_dihedral_angle_4_deg13.829
r_dihedral_angle_1_deg7.358
r_long_range_B_refined6.863
r_long_range_B_other6.839
r_angle_refined_deg2.018
r_scangle_other1.865
r_mcangle_it1.521
r_mcangle_other1.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.956
r_dihedral_angle_3_deg19.235
r_dihedral_angle_4_deg13.829
r_dihedral_angle_1_deg7.358
r_long_range_B_refined6.863
r_long_range_B_other6.839
r_angle_refined_deg2.018
r_scangle_other1.865
r_mcangle_it1.521
r_mcangle_other1.521
r_angle_other_deg1.21
r_scbond_it1.081
r_scbond_other1.081
r_mcbond_it0.859
r_mcbond_other0.859
r_chiral_restr0.113
r_bond_refined_d0.019
r_bond_other_d0.01
r_gen_planes_refined0.01
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 Atoms3920
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing