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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 PDB 1XD5
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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.96 α = 84.24 b = 42.36 β = 85.91 c = 56.99 γ = 84.81
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 2011-01-10 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 2.25 40 94.2 0.103 10 3.8 9500
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 2.25 2.37 92.3 0.3 3.8 1365
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 1xd5 2.25 35.36 8839 659 94.23 0.22475 0.2217 0.2214 0.26458 0.2632 RANDOM 18.519
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] 0.28 -0.5 -0.01 0.38 2.2 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.248 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 16.984 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.434 r_scbond_it 2.386 r_angle_refined_deg 1.758 r_mcangle_it 1.522 r_mcbond_it 0.886 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.248 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 16.984 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.434 r_scbond_it 2.386 r_angle_refined_deg 1.758 r_mcangle_it 1.522 r_mcbond_it 0.886 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1622 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling