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Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) from the yeast Saccharomyces cerevisiae, in complex with calcium and mannose
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 5 293 Protein solution: 50 mM sodium acetate pH 5, 150 mM NaCl, 10 mM CaCl2
Crystallization condition: 1 M NaCl, 15% v/v EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.7 α = 90 b = 63.59 β = 90 c = 106.54 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 298 CCD RIGAKU SATURN 944+ 2013-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.12 15.37 90.1 0.1 12.3 5.7 16718 16718
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 2.12 2.23 80.3 0.433 3.7 5.6 2106
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 2.12 15.03 15840 15840 839 89.56 0.14838 0.14838 0.14602 0.16 0.19405 0.1958 RANDOM 26.134
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] 0.04 -0.32 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_3_deg 14.76 r_dihedral_angle_4_deg 8.719 r_dihedral_angle_1_deg 6.523 r_angle_refined_deg 2.086 r_angle_other_deg 0.898 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_3_deg 14.76 r_dihedral_angle_4_deg 8.719 r_dihedral_angle_1_deg 6.523 r_angle_refined_deg 2.086 r_angle_other_deg 0.898 r_chiral_restr 0.114 r_bond_refined_d 0.02 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 13
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing REFMAC refinement XDS data reduction Aimless data scaling