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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 7.5 298 1.2M tri-sodium citrate, 0.1M Na HEPES, 6% glycerol, 30%(w/v) 1,5 diammino pentane dihydrochloride, 60mM mannose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 90 b = 80.08 β = 105.98 c = 56.91 γ = 90
Symmetry Space Group P 1 21 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 2012-03-11 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 2.24 40 98.7 0.112 6.2 2.7 47027 19379
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 2.24 2.36 97.2 0.38 2.3 2766
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 2.24 40 18340 993 98.7 0.22216 0.21999 0.2253 0.26108 0.2622 RANDOM 22.834
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] 2.73 0.75 -1.91 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_4_deg 14.406 r_dihedral_angle_1_deg 6.752 r_scangle_it 1.302 r_angle_refined_deg 1.116 r_scbond_it 0.785 r_mcangle_it 0.59 r_mcbond_it 0.318 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_4_deg 14.406 r_dihedral_angle_1_deg 6.752 r_scangle_it 1.302 r_angle_refined_deg 1.116 r_scbond_it 0.785 r_mcangle_it 0.59 r_mcbond_it 0.318 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 132
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling