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Structure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-Flo1p) from the yeast Saccharomyces pastorianus, in complex with calcium and alpha-1,2-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XJQ PDB ENTRY 2XJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2
Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M imidazole-MES pH 6.5, 30% w/v PEG 550 MME - PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.618 α = 90 b = 85.476 β = 93.72 c = 68.24 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 PIXEL DECTRIS PILATUS 6M 2012-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
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 1.73 38.54 97.3 0.092 9.9 4.5 44852 44852
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 1.73 1.76 96 0.704 2.1 4.7 2430
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2XJQ 1.73 35.13 42548 42548 2275 97.12 0.14023 0.14023 0.13741 0.1403 0.19329 0.1939 RANDOM 22.116
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] 0.19 -0.05 0.07 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_sphericity_free 31.222 r_sphericity_bonded 13.206 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_4_deg 10.724 r_dihedral_angle_1_deg 6.812 r_rigid_bond_restr 4.945 r_angle_refined_deg 1.829 r_angle_other_deg 1.13 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_sphericity_free 31.222 r_sphericity_bonded 13.206 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_4_deg 10.724 r_dihedral_angle_1_deg 6.812 r_rigid_bond_restr 4.945 r_angle_refined_deg 1.829 r_angle_other_deg 1.13 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 48
Software Software Software Name Purpose BALBES phasing REFMAC refinement XDS data reduction Aimless data scaling