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Crystal structure of L. decastes alpha-galactosyl-binding lectin, orthorhombic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NDS PDB ENTRY 4NDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.365 α = 90 b = 44.23 β = 90 c = 62.133 γ = 90
Symmetry Space Group P 2 2 21
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 ADSC QUANTUM 4r 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.03 20 97.5 0.061 13.93 50532 50528 -3 7.38
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 1.03 1.09 86.6 0.59 1.61
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4NDS 1.03 18.756 1.99 50528 50408 2531 97.55 0.1152 0.1142 0.1352 0.1345 11.078
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.771 f_angle_d 1.48 f_chiral_restr 0.083 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 722 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction XDS data scaling