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Photorhabdus asymbiotica lectin PHL in complex with O-methylated PGL-1-derived disaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 4M NaCl, 100mM Hepes, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.86 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.893 α = 90 b = 80.893 β = 90 c = 113.642 γ = 120
Symmetry Space Group P 31 2 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 PILATUS3 2M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.75 44.13 100 0.073 0.999 17 11.1 44002 28.891
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 1.75 1.84 100 1.128 0.723 2.2 11.1
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 5MXE 1.75 40.48 41752 2209 99.99 0.18479 0.18345 0.1906 0.20972 0.2158 RANDOM 29.377
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] 0.44 0.22 0.44 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.226 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_4_deg 10.35 r_dihedral_angle_1_deg 8.405 r_long_range_B_refined 3.635 r_long_range_B_other 3.475 r_scangle_other 2.207 r_mcangle_it 1.963 r_mcangle_other 1.962 r_scbond_it 1.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.226 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_4_deg 10.35 r_dihedral_angle_1_deg 8.405 r_long_range_B_refined 3.635 r_long_range_B_other 3.475 r_scangle_other 2.207 r_mcangle_it 1.963 r_mcangle_other 1.962 r_scbond_it 1.516 r_scbond_other 1.516 r_mcbond_other 1.299 r_mcbond_it 1.298 r_angle_refined_deg 1.27 r_angle_other_deg 1.262 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 2654 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing