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Crystal Structure of Vibrio cholerae PilU, a PilT-dependent Retraction ATPase - Crystal Form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 Protein: 15.0 mg/ml, 0.5M Sodium chloride, 1mM TCEP;
Screen: AmSO4 (B1), 0.2 M Cadmium sulfate, 2.2 M Ammonium sulfate;
Cryo: 2M Lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.835 α = 90 b = 120.826 β = 90 c = 175.559 γ = 90
Symmetry Space Group I 2 2 2
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 MARMOSAIC 300 mm CCD 2023-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.7 30 100 0.141 0.141 0.152 0.056 0.996 16.1 7.5 30441 -3 41.6
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 2.7 2.75 100 0.537 0.697 1.8 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.7 29.58 26612 1386 92.07 0.22509 0.22274 0.2218 0.27018 0.2724 RANDOM 48.83
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] -0.08 0.83 -0.75
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.549 r_long_range_B_other 7.272 r_dihedral_angle_3_deg 3.806 r_scangle_other 3.701 r_mcangle_it 2.87 r_mcangle_other 2.87 r_scbond_it 2.345 r_scbond_other 2.143 r_mcbond_it 1.685 r_mcbond_other 1.683
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.549 r_long_range_B_other 7.272 r_dihedral_angle_3_deg 3.806 r_scangle_other 3.701 r_mcangle_it 2.87 r_mcangle_other 2.87 r_scbond_it 2.345 r_scbond_other 2.143 r_mcbond_it 1.685 r_mcbond_other 1.683 r_dihedral_angle_1_deg 1.33 r_angle_refined_deg 1.296 r_dihedral_angle_2_deg 0.66 r_angle_other_deg 0.471 r_chiral_restr 0.066 r_gen_planes_refined 0.015 r_gen_planes_other 0.013 r_bond_refined_d 0.003 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 8245 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 275
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing