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Crystal structure of the lectin LecA from Pseudomonas aeruginosa in complex with a phenyl-epoxy-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 292 25% peg 2KMME 100mM sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.01 38.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.343 α = 90 b = 73.771 β = 93.36 c = 101.454 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 315r 2015-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 27.3 98.9 0.043 0.999 19.8 3.6 36960 2 9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 96.1 0.193 0.954 5.2 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1OKO 1.8 27.3 35035 1907 98.89 0.1509 0.14853 0.1599 0.19362 0.2036 RANDOM 15.187
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] 1.24 1.13 -1.19 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_3_deg 10.401 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 4.468 r_long_range_B_other 4.197 r_scangle_other 2.849 r_mcangle_it 1.899 r_mcangle_other 1.898 r_scbond_it 1.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_3_deg 10.401 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 4.468 r_long_range_B_other 4.197 r_scangle_other 2.849 r_mcangle_it 1.899 r_mcangle_other 1.898 r_scbond_it 1.841 r_scbond_other 1.84 r_angle_refined_deg 1.662 r_mcbond_it 1.296 r_mcbond_other 1.296 r_angle_other_deg 1.076 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 3604 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing