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Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.1 M MES monohydrate pH 6.0,
22% v/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.69 α = 90 b = 60.39 β = 99.13 c = 82.98 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 IMAGE PLATE RIGAKU RAXIS IV++ 2020-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 1.9 30.19 98 0.13 0.97 7 4 28551
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 1.9 2 0.18 0.88
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7VS6 1.9 24.896 28548 1468 98.012 0.22 0.2185 0.2244 0.2485 0.2515 13.985
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] 1.64 -0.141 -1.233 -0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.329 r_dihedral_angle_4_deg 14.331 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_1_deg 8.18 r_lrange_it 4.388 r_lrange_other 4.382 r_angle_other_deg 2.35 r_scangle_other 2.202 r_scangle_it 2.201 r_mcangle_other 1.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.329 r_dihedral_angle_4_deg 14.331 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_1_deg 8.18 r_lrange_it 4.388 r_lrange_other 4.382 r_angle_other_deg 2.35 r_scangle_other 2.202 r_scangle_it 2.201 r_mcangle_other 1.893 r_mcangle_it 1.892 r_angle_refined_deg 1.567 r_scbond_it 1.44 r_scbond_other 1.437 r_mcbond_it 1.192 r_mcbond_other 1.189 r_nbd_other 0.373 r_symmetry_nbd_refined 0.254 r_symmetry_xyhbond_nbd_refined 0.251 r_symmetry_nbd_other 0.225 r_nbd_refined 0.183 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_ncsr_local_group_1 0.044 r_symmetry_xyhbond_nbd_other 0.036 r_bond_other_d 0.035 r_chiral_restr_other 0.021 r_gen_planes_other 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2423 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing