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Crystal structure of the outer membrane lipoprotein OprI from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG 200, 0.1 M MES pH 6.5 and 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.88 34.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.6 α = 90 b = 52.6 β = 90 c = 52.6 γ = 90
Symmetry Space Group P 21 3
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 EIGER X 4M 2025-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.1 52.6 97.2 0.038 13 17.5 2916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.383
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 2.101 37.194 2886 146 96.522 0.254 0.2538 0.2607 0.2667 0.2694 60.565
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.261 r_dihedral_angle_2_deg 15.313 r_dihedral_angle_6_deg 15.041 r_lrange_it 9.128 r_lrange_other 9.125 r_mcangle_it 5.983 r_mcangle_other 5.972 r_scangle_it 5.67 r_scangle_other 5.661 r_dihedral_angle_1_deg 4.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.261 r_dihedral_angle_2_deg 15.313 r_dihedral_angle_6_deg 15.041 r_lrange_it 9.128 r_lrange_other 9.125 r_mcangle_it 5.983 r_mcangle_other 5.972 r_scangle_it 5.67 r_scangle_other 5.661 r_dihedral_angle_1_deg 4.421 r_mcbond_it 3.641 r_mcbond_other 3.641 r_scbond_it 3.431 r_scbond_other 3.423 r_angle_refined_deg 1.219 r_angle_other_deg 0.465 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.239 r_symmetry_nbd_other 0.207 r_nbd_other 0.177 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.052 r_symmetry_xyhbond_nbd_refined 0.043 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 433 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing