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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 8.2 293 sodium phosphate monohydrate, potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 1.84 33.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.692 α = 90 b = 44.121 β = 128.34 c = 77.503 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 PILATUS3 S 6M 2023-12-01 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 2.34 40.31 98.8 0.133 0.144 0.054 0.997 11.8 6.8 11521
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 2.34 2.42 97.7 0.829 0.895 0.335 0.744 7
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 2.34 40.31 10951 569 98.47 0.19088 0.18724 0.1938 0.25872 0.259 RANDOM 36.674
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] -0.04 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.243 r_dihedral_angle_4_deg 21.361 r_dihedral_angle_3_deg 18.607 r_dihedral_angle_1_deg 8.658 r_long_range_B_refined 7.103 r_long_range_B_other 7.102 r_scangle_other 5.071 r_mcangle_it 4.797 r_mcangle_other 4.797 r_scbond_it 3.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.243 r_dihedral_angle_4_deg 21.361 r_dihedral_angle_3_deg 18.607 r_dihedral_angle_1_deg 8.658 r_long_range_B_refined 7.103 r_long_range_B_other 7.102 r_scangle_other 5.071 r_mcangle_it 4.797 r_mcangle_other 4.797 r_scbond_it 3.354 r_scbond_other 3.353 r_mcbond_it 3.161 r_mcbond_other 3.153 r_angle_refined_deg 1.596 r_angle_other_deg 1.237 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 2169 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing