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Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M MES pH 6.5, 12% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.815 α = 90 b = 56.937 β = 104.86 c = 60.695 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.980 ESRF ID23-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 46.22 98.86 0.07178 0.02739 0.999 17.06 6.7 41326 23.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.657 99.9 0.6474 0.561 1.32 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5B5Q 1.6 46.22 39198 2021 98.88 0.17122 0.16955 0.1845 0.20333 0.2161 RANDOM 23.148
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] -0.12 0.35 -0.19 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.692 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 14.026 r_long_range_B_refined 6.377 r_long_range_B_other 6.376 r_dihedral_angle_1_deg 6.224 r_scangle_other 4.544 r_scbond_it 3.047 r_scbond_other 3.046 r_angle_refined_deg 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.692 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 14.026 r_long_range_B_refined 6.377 r_long_range_B_other 6.376 r_dihedral_angle_1_deg 6.224 r_scangle_other 4.544 r_scbond_it 3.047 r_scbond_other 3.046 r_angle_refined_deg 2.53 r_mcangle_it 2.301 r_mcangle_other 2.3 r_mcbond_it 1.64 r_mcbond_other 1.638 r_angle_other_deg 1.287 r_chiral_restr 0.19 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing