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Japanese Marasmius oreades lectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate, 1.0 M Lithium sulfate monohydrate, 5% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.395 α = 90 b = 57.395 β = 90 c = 57.944 γ = 120
Symmetry Space Group P 32 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 CCD RIGAKU SATURN A200 2012-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SAGA-LS BEAMLINE BL07 1.2 SAGA-LS BL07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.4 14.38 99 9.2 10.28 22065
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 1XD6 1.4 14.38 20807 1119 98.24 0.14751 0.14437 0.21027 0.2421 RANDOM 18.369
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 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 64.286 r_dihedral_angle_2_deg 30.085 r_sphericity_bonded 21.958 r_dihedral_angle_4_deg 13.852 r_dihedral_angle_3_deg 11.368 r_long_range_B_refined 8.316 r_scangle_other 6.99 r_long_range_B_other 6.618 r_rigid_bond_restr 6.149 r_dihedral_angle_1_deg 6.036
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 64.286 r_dihedral_angle_2_deg 30.085 r_sphericity_bonded 21.958 r_dihedral_angle_4_deg 13.852 r_dihedral_angle_3_deg 11.368 r_long_range_B_refined 8.316 r_scangle_other 6.99 r_long_range_B_other 6.618 r_rigid_bond_restr 6.149 r_dihedral_angle_1_deg 6.036 r_scbond_it 5.866 r_scbond_other 5.792 r_mcangle_other 4.07 r_mcangle_it 4.053 r_mcbond_it 3.179 r_mcbond_other 3.125 r_angle_refined_deg 1.819 r_angle_other_deg 0.796 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 916 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement