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Dimeric Structure of ConA/M2P-Man
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M Sodium chloride, 0.1M Phosphate-citrate pH 4.2 10% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.216 α = 90 b = 79.07 β = 117.2 c = 87.917 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 PIXEL DECTRIS EIGER X 16M 2024-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979 SSRF BL10U2
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 2.17 78.2 99.8 0.136 0.161 0.084 0.983 4.4 3.5 52760
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 2.17 2.28 99.4 0.862 1.058 0.602 0.369 2.9
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 4P9W 2.17 78.2 49425 2477 98.22 0.21093 0.2087 0.2142 0.2569 0.2611 RANDOM 27.965
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] 0.01 0.02 -0.11 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.228 r_dihedral_angle_4_deg 20.613 r_dihedral_angle_3_deg 14.739 r_dihedral_angle_1_deg 8.818 r_long_range_B_refined 7.03 r_long_range_B_other 7.029 r_mcangle_it 4.694 r_mcangle_other 4.694 r_scangle_other 4.301 r_mcbond_it 2.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.228 r_dihedral_angle_4_deg 20.613 r_dihedral_angle_3_deg 14.739 r_dihedral_angle_1_deg 8.818 r_long_range_B_refined 7.03 r_long_range_B_other 7.029 r_mcangle_it 4.694 r_mcangle_other 4.694 r_scangle_other 4.301 r_mcbond_it 2.751 r_mcbond_other 2.75 r_scbond_it 2.583 r_scbond_other 2.581 r_angle_refined_deg 1.599 r_angle_other_deg 1.222 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 7236 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing