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Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293.15 0.2 M calcium acetate, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.88 34.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.92 α = 90 b = 64.75 β = 91.26 c = 64.47 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 CCD ADSC QUANTUM 210r 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.9 37.24 98.1 0.078 0.044 0.997 12.2 4 40168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 82.1 0.267 0.177 0.898 4.1 3.2 2128
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 3I8T 1.9 37.24 38075 2016 97.89 0.1574 0.1552 0.1663 0.1987 0.2051 RANDOM 17.307
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] -0.17 0.1 0.74 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.216 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_4_deg 13.055 r_dihedral_angle_1_deg 7.023 r_mcangle_it 2.52 r_mcbond_it 1.74 r_mcbond_other 1.731 r_angle_refined_deg 1.063 r_angle_other_deg 0.514 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.216 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_4_deg 13.055 r_dihedral_angle_1_deg 7.023 r_mcangle_it 2.52 r_mcbond_it 1.74 r_mcbond_other 1.731 r_angle_refined_deg 1.063 r_angle_other_deg 0.514 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4408 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 104
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing