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Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.0M ammonium citrate tribasic, 0.1M bis-tris propane, 60mM methyl-alpha-mannose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.51 α = 90 b = 80.86 β = 130.69 c = 100.94 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2012-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.4 40 98.4 0.156 6 3.7 10344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.58 98.1 0.43 3.7 1500
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 Native structure 3.4 40 9835 494 98.26 0.2443 0.242 0.2409 0.2882 0.2809 RANDOM 75.581
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] -3.23 -4.56 2.52 3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_4_deg 10.094 r_dihedral_angle_1_deg 5.076 r_angle_refined_deg 0.786 r_mcangle_it 0.681 r_angle_other_deg 0.663 r_mcbond_it 0.368 r_mcbond_other 0.368 r_chiral_restr 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_4_deg 10.094 r_dihedral_angle_1_deg 5.076 r_angle_refined_deg 0.786 r_mcangle_it 0.681 r_angle_other_deg 0.663 r_mcbond_it 0.368 r_mcbond_other 0.368 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3951 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 78
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling