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Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Gala1-3Gal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AF9 PRUNED VERSION OF PDB ENTRY 4AF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.01 M SODIUM ACETATE PH 4.6, 30% PEG4000, 0.2 M AMMONIUM ACETATE, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALA1-3GAL
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.52 α = 90 b = 63.29 β = 90 c = 110.3 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 PIXEL DECTRIS PILATUS 6M 2013-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.5 41.58 99.9 0.05 20.7 5.4 47367 -3
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 1.5 1.58 99.9 0.52 3 5.2
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 PRUNED VERSION OF PDB ENTRY 4AF9 1.5 41.58 46100 1223 99.78 0.15034 0.14965 0.1599 0.17661 0.1774 RANDOM 20.24
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] -0.24 0.6 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.362 r_sphericity_free 35.138 r_dihedral_angle_3_deg 12.079 r_sphericity_bonded 10.133 r_dihedral_angle_4_deg 8.011 r_dihedral_angle_1_deg 5.893 r_mcangle_it 1.698 r_scbond_it 1.516 r_mcbond_it 1.35 r_mcbond_other 1.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.362 r_sphericity_free 35.138 r_dihedral_angle_3_deg 12.079 r_sphericity_bonded 10.133 r_dihedral_angle_4_deg 8.011 r_dihedral_angle_1_deg 5.893 r_mcangle_it 1.698 r_scbond_it 1.516 r_mcbond_it 1.35 r_mcbond_other 1.314 r_angle_refined_deg 1.201 r_rigid_bond_restr 1.141 r_angle_other_deg 0.718 r_chiral_restr 0.074 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_mcangle_other 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 1817 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing