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Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside
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 7.5 293 4.7 M NaCl, 100 mM Hepes
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.346 α = 90 b = 81.346 β = 90 c = 222.783 γ = 120
Symmetry Space Group P 32 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 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8943 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 1.86 44.56 99.9 0.193 0.996 12.5 11.1 69572
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 1.86 1.96 99.2 1.383 0.576 1.8 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 1.86 44.56 69572 3505 99.94 0.18258 0.18095 0.1894 0.21536 0.2229 RANDOM 20.71
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] 0.22 0.11 0.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_3_deg 12.211 r_dihedral_angle_4_deg 10.491 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 3.561 r_long_range_B_other 3.31 r_scangle_other 2.029 r_angle_refined_deg 1.466 r_mcangle_it 1.462 r_mcangle_other 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_3_deg 12.211 r_dihedral_angle_4_deg 10.491 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 3.561 r_long_range_B_other 3.31 r_scangle_other 2.029 r_angle_refined_deg 1.466 r_mcangle_it 1.462 r_mcangle_other 1.462 r_scbond_it 1.221 r_scbond_other 1.221 r_angle_other_deg 0.945 r_mcbond_it 0.914 r_mcbond_other 0.914 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 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 5304 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing