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Photorhabdus asymbiotica lectin (PHL) in complex with blood group H trisaccharide
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, SITTING DROP 7.5 290 3.7-4.3 M NaCl, 100 mM Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.309 α = 90 b = 80.309 β = 90 c = 112.973 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 CCD RAYONIX MX-225 2015-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.895 BESSY 14.3
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 2.2 43.85 100 0.085 0.999 23.8 12.4 21984
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 2.2 2.32 98 0.742 0.885 3.8 12.5
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 2.2 43.85 20916 1035 99.98 0.18732 0.18529 0.1905 0.22842 0.2282 RANDOM 40.284
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] 0.58 0.29 0.58 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_4_deg 8.259 r_dihedral_angle_1_deg 7.479 r_long_range_B_refined 5.262 r_long_range_B_other 5.261 r_scangle_other 3.952 r_mcangle_it 3.569 r_mcangle_other 3.567 r_scbond_it 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_4_deg 8.259 r_dihedral_angle_1_deg 7.479 r_long_range_B_refined 5.262 r_long_range_B_other 5.261 r_scangle_other 3.952 r_mcangle_it 3.569 r_mcangle_other 3.567 r_scbond_it 2.653 r_scbond_other 2.652 r_mcbond_it 2.47 r_mcbond_other 2.47 r_angle_refined_deg 1.511 r_angle_other_deg 0.971 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2658 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing