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Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose-3'-sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 1.2 M ammonium sulfate, 0.1 M HEPES, 4 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.12 36.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.224 α = 90 b = 129.208 β = 96.88 c = 45.233 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 315r 2014-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.1 44.91 98.4 0.111 0.045 0.995 12.5 5.5 29564
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 2.1 2.16 96.8 0.181 0.107 0.89 6.4 3.7 2426
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 3OJB 2.1 42.42 28144 1388 98.21 0.163 0.1607 0.1696 0.2103 0.2163 RANDOM 28.064
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] -4.48 6.25 3.51 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.802 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_4_deg 13.066 r_dihedral_angle_1_deg 7.029 r_mcangle_it 2.004 r_angle_refined_deg 1.346 r_angle_other_deg 1.223 r_mcbond_it 1.127 r_mcbond_other 1.127 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.802 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_4_deg 13.066 r_dihedral_angle_1_deg 7.029 r_mcangle_it 2.004 r_angle_refined_deg 1.346 r_angle_other_deg 1.223 r_mcbond_it 1.127 r_mcbond_other 1.127 r_chiral_restr 0.101 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4350 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing