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Crystal structure of the truncated P1 pilin from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A3RJ49-F1 Model was split into compact region using pLDDT scores and the "Process Predicted Models" tool on ccp4i2 (1 and 14-18, 2-13 and 79-90 and 105-124, 19-48, 49-64 and 75-78, 65-74 and 92-104)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 35% PEG8000, 100 mM sodium cacodylate, 200 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 1.77 30.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.453 α = 90 b = 54.853 β = 96.145 c = 37.772 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 315 2003-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0236 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 0.94 54.9 99.5 0.141 0.158 0.069 0.988 14.2 4 22344 10.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 99.2 0.498 0.615 0.355 0.639 3.9 2.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 37.555 22324 682 99.492 0.132 0.1306 0.1307 0.1738 0.1738 Random 10.936
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] -0.134 0.209 0.33 -0.236
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.118 r_dihedral_angle_6_deg 14.375 r_lrange_other 13.032 r_dihedral_angle_2_deg 11.78 r_dihedral_angle_3_deg 11.033 r_scangle_it 6.883 r_scangle_other 6.878 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.751 r_scbond_other 4.746
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.118 r_dihedral_angle_6_deg 14.375 r_lrange_other 13.032 r_dihedral_angle_2_deg 11.78 r_dihedral_angle_3_deg 11.033 r_scangle_it 6.883 r_scangle_other 6.878 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.751 r_scbond_other 4.746 r_mcangle_it 4.7 r_mcangle_other 4.697 r_rigid_bond_restr 3.812 r_mcbond_it 3.201 r_mcbond_other 3.199 r_angle_refined_deg 1.916 r_angle_other_deg 0.664 r_nbd_other 0.269 r_xyhbond_nbd_refined 0.261 r_nbd_refined 0.227 r_symmetry_nbd_other 0.21 r_symmetry_nbd_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_other 0.167 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 915 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing