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Crystal structure of recombinant mushroom Agaricus bisporus mannose-binding protein with a longer C-terminal region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 sodium formate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.164 α = 90 b = 43.982 β = 90 c = 67.247 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2024-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.51 43.98 100 0.048 0.052 0.021 1 21.3 6.2 19365
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 1.51 1.54 100 0.649 0.743 0.356 0.778 4.2
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 5EHA 1.51 36.81 18393 925 99.96 0.13511 0.13199 0.1453 0.19376 0.2014 RANDOM 23.837
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] 0.53 -0.27 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.797 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 14.816 r_dihedral_angle_1_deg 8.725 r_long_range_B_refined 8.218 r_long_range_B_other 8.205 r_scangle_other 7.559 r_mcangle_other 6.888 r_mcangle_it 6.887 r_scbond_it 6.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.797 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 14.816 r_dihedral_angle_1_deg 8.725 r_long_range_B_refined 8.218 r_long_range_B_other 8.205 r_scangle_other 7.559 r_mcangle_other 6.888 r_mcangle_it 6.887 r_scbond_it 6.713 r_scbond_other 6.709 r_mcbond_it 5.732 r_mcbond_other 5.698 r_rigid_bond_restr 4.512 r_angle_refined_deg 1.365 r_angle_other_deg 1.353 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1204 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing