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Marasmius oreades agglutinin (MOA) activated by manganese (II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.1 M cacodylate/HCl pH 6.5, 16% PEG 8000, 0.15M sodium acetate, 5 mM MnCl2, 12.5% DMSO, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 3.3 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.952 α = 90 b = 120.952 β = 90 c = 99.477 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 225 mm CCD 2012-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.85051 ESRF ID23-1
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 1.85 46.3 90.2 0.046 0.055 0.03 0.998 22.8 3.9 63674
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 1.85 1.89 57.8 0.256 0.361 0.256 0.853 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3EF2 1.85 46.3 34498 1728 93.137 0.157 0.1558 0.1676 0.1824 0.191 17.957
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] 0.518 0.259 0.518 -1.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_3_deg 13.521 r_dihedral_angle_4_deg 10.317 r_dihedral_angle_1_deg 8.814 r_lrange_it 4.117 r_lrange_other 4.037 r_scangle_it 3.136 r_scangle_other 3.135 r_scbond_it 2.065 r_scbond_other 2.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_3_deg 13.521 r_dihedral_angle_4_deg 10.317 r_dihedral_angle_1_deg 8.814 r_lrange_it 4.117 r_lrange_other 4.037 r_scangle_it 3.136 r_scangle_other 3.135 r_scbond_it 2.065 r_scbond_other 2.065 r_mcangle_it 1.826 r_mcangle_other 1.826 r_mcbond_it 1.357 r_mcbond_other 1.357 r_angle_refined_deg 0.815 r_symmetry_xyhbond_nbd_other 0.796 r_angle_other_deg 0.606 r_symmetry_metal_ion_refined 0.482 r_metal_ion_refined 0.351 r_symmetry_nbd_refined 0.263 r_nbd_refined 0.251 r_nbd_other 0.235 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.104 r_gen_planes_refined 0.041 r_gen_planes_other 0.034 r_bond_refined_d 0.013 r_chiral_restr 0.012 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2280 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing