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Crystal Structure of Tarin Lectin bound to Trimannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 25-35% Peg 3350, 0.2M Lithium Sulfate, 0.1M Hepes
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.28 α = 76.19 b = 78.828 β = 70.44 c = 92.935 γ = 59.8
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 RAYONIX MX-300 mirrors 2008-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.91 50 97.3 0.085 6.5 3.9 135823
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 1.91 1.94 83.6 0.352 3.5
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 5T1X 1.91 45.05 135821 6809 97.13 0.2108 0.2091 0.2022 0.2441 0.2385 RANDOM 18.8838
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] -0.3137 -0.9815 -0.251 1.8786 -0.0256 -1.5649
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.32 t_other_torsion 2.42 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.32 t_other_torsion 2.42 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13570 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 544
Software Software Software Name Purpose HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling BUSTER refinement PHASER phasing DENZO data reduction SCALEPACK data scaling