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Human antibody (Fab) and P. aeruginosa (T3SS) protein PcrV-fragment complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold ColabFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Micro-seeding, 0.1 M Sodium Acetate pH 5, 25% PEG 1000, 0.001M ZnCl2
Crystal Properties Matthews coefficient Solvent content 3.25 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.582 α = 90 b = 92.308 β = 104.828 c = 105.22 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 PIXEL DECTRIS PILATUS 2M 2023-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.559 49.21 99.5 0.2 0.977 5.02 3.38 52157 45.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.71 99.2 1.53 0.312 0.72 3.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.56 49.21 52157 2086 99.54 0.211 0.2097 0.2159 0.237 0.2416 46.739
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] 0.306 -0.474 -0.233 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.825 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 7.449 r_lrange_it 6.67 r_lrange_other 6.646 r_dihedral_angle_2_deg 5.495 r_scangle_it 4.588 r_scangle_other 4.588 r_mcangle_it 3.543 r_mcangle_other 3.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.825 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 7.449 r_lrange_it 6.67 r_lrange_other 6.646 r_dihedral_angle_2_deg 5.495 r_scangle_it 4.588 r_scangle_other 4.588 r_mcangle_it 3.543 r_mcangle_other 3.543 r_scbond_it 2.81 r_scbond_other 2.81 r_mcbond_it 2.154 r_mcbond_other 2.152 r_angle_refined_deg 1.266 r_angle_other_deg 0.456 r_xyhbond_nbd_refined 0.243 r_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_nbd_other 0.183 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.109 r_symmetry_xyhbond_nbd_other 0.102 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.055 r_ncsr_local_group_3 0.051 r_ncsr_local_group_2 0.042 r_ncsr_local_group_1 0.027 r_gen_planes_refined 0.013 r_gen_planes_other 0.012 r_bond_refined_d 0.006 r_ext_dist_refined_b 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8596 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing