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Dioclea megacarpa lectin (DmegA) complexed with X-Man
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GDF Dioclea violacea lectin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 0.5% PEGME 5000
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.35 α = 90 b = 109.414 β = 90 c = 126.364 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 2M 2022-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.46 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 46.661 100 0.088 0.092 0.025 1 21.6 13.1 31790
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 1.148 1.193 0.322 0.853 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.2 46.661 31752 1593 99.852 0.203 0.2006 0.2085 0.2483 0.2543 50.893
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] -0.02 0.007 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.591 r_dihedral_angle_6_deg 16.566 r_dihedral_angle_3_deg 13.958 r_lrange_it 9.756 r_lrange_other 9.745 r_dihedral_angle_1_deg 8.496 r_scangle_it 7.22 r_scangle_other 7.219 r_mcangle_other 6.135 r_mcangle_it 6.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.591 r_dihedral_angle_6_deg 16.566 r_dihedral_angle_3_deg 13.958 r_lrange_it 9.756 r_lrange_other 9.745 r_dihedral_angle_1_deg 8.496 r_scangle_it 7.22 r_scangle_other 7.219 r_mcangle_other 6.135 r_mcangle_it 6.134 r_scbond_it 4.956 r_scbond_other 4.955 r_mcbond_it 4.372 r_mcbond_other 4.368 r_angle_refined_deg 1.477 r_angle_other_deg 0.498 r_nbd_refined 0.222 r_symmetry_nbd_other 0.205 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.182 r_metal_ion_refined 0.161 r_xyhbond_nbd_refined 0.149 r_nbd_other 0.148 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3548 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing Coot model building