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Crystal Structure of N-terminal domain of human galectin-8 with D-lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M bis-tris, 25% PEG3350, 1mM lactose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.913 α = 90 b = 50.551 β = 90 c = 69.336 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU JUPITER 210 mirrors 2006-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.13 50 99.7 0.074 32.8 6.56 9421 -3 5.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.21 99.2 0.13 12.6
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 2YV8 2.13 33.99 9191 494 97.3 0.19 0.19 0.182 0.234 0.2218 RANDOM 15.6
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] 3.56 -0.78 -2.78
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 2.74 c_scbond_it 2.03 c_mcangle_it 1.85 c_angle_deg 1.3 c_mcbond_it 1.27 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 2.74 c_scbond_it 2.03 c_mcangle_it 1.85 c_angle_deg 1.3 c_mcbond_it 1.27 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1180 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 23
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing