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Structure of ConA/IMI-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 buffer: 20 mM HEPES, 5 mM CaCl2, 5 mM MnCl2; pH = 7.2, precipitant: Ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 4.34 71.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.38 α = 90 b = 113.72 β = 127.27 c = 83.71 γ = 90
Symmetry Space Group C 1 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 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 2.48 28.76 99.6 0.062 0.068 0.027 0.998 18 5.8 30883
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 2.48 2.54 96.9 0.547 0.631 0.306 0.636 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P9W 2.48 28.76 28944 1472 98.03 0.18949 0.18754 0.22756 0.228 RANDOM 52.585
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 -0.02 0.08 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_3_deg 15.634 r_dihedral_angle_4_deg 14.531 r_long_range_B_refined 10.468 r_long_range_B_other 10.467 r_dihedral_angle_1_deg 9.577 r_scangle_other 8.039 r_mcangle_it 7.522 r_mcangle_other 7.52 r_scbond_it 5.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_3_deg 15.634 r_dihedral_angle_4_deg 14.531 r_long_range_B_refined 10.468 r_long_range_B_other 10.467 r_dihedral_angle_1_deg 9.577 r_scangle_other 8.039 r_mcangle_it 7.522 r_mcangle_other 7.52 r_scbond_it 5.531 r_scbond_other 5.529 r_mcbond_it 5.098 r_mcbond_other 5.097 r_angle_refined_deg 1.851 r_angle_other_deg 1.252 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 3618 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing