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Structural and functional analysis of the Pseudomonas aeruginosa PA1677 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Sodium HEPES; MOPS (acid) 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 0.2M DL-Glutamic acid monohydrate; 0.2M DL Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.284 α = 90 b = 245.26 β = 90 c = 126.262 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 6M 2021-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 1.78 122.63 96.2 0.263 0.285 0.107 0.989 6.7 7 120918
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 1.78 1.88 73.9 1.302 1.462 0.643 0.416 4.4
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 1.78 122.63 114353 6093 95.87 0.1759 0.17416 0.1881 0.20836 0.2173 RANDOM 22.632
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] 0.75 -0.62 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 19.318 r_dihedral_angle_3_deg 13.581 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 6.683 r_long_range_B_other 6.378 r_scangle_other 4.631 r_scbond_it 2.888 r_scbond_other 2.888 r_mcangle_it 2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 19.318 r_dihedral_angle_3_deg 13.581 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 6.683 r_long_range_B_other 6.378 r_scangle_other 4.631 r_scbond_it 2.888 r_scbond_other 2.888 r_mcangle_it 2.881 r_mcangle_other 2.881 r_mcbond_it 1.859 r_mcbond_other 1.858 r_angle_refined_deg 1.586 r_angle_other_deg 1.564 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8804 Nucleic Acid Atoms Solvent Atoms 947 Heterogen Atoms 62
Software Software Software Name Purpose Aimless data scaling REFMAC refinement autoPROC data reduction PHASER phasing