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Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Lactose
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 0.08 M SODIUM ACETATE PH:4.6, 1.6 M AMMONIUM SULFATE, 20% GLYCEROL, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.3 α = 90 b = 61.1 β = 90 c = 106.3 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 CCD MARRESEARCH MARMOSAIC 255 MM 2012-09-16 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 1.48 28.77 99.7 0.04 21.1 3.8 45573 -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 1.48 1.56 99.9 0.57 2.9 3.8
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 1.48 26.5 44337 1173 99.63 0.145 0.14427 0.1575 0.17152 0.1844 RANDOM 19.167
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] 0.5 -0.13 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_sphericity_free 30.678 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_4_deg 8.761 r_sphericity_bonded 8.656 r_dihedral_angle_1_deg 6.507 r_rigid_bond_restr 2.211 r_mcangle_it 2.133 r_scbond_it 2.057 r_mcbond_it 1.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_sphericity_free 30.678 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_4_deg 8.761 r_sphericity_bonded 8.656 r_dihedral_angle_1_deg 6.507 r_rigid_bond_restr 2.211 r_mcangle_it 2.133 r_scbond_it 2.057 r_mcbond_it 1.757 r_mcbond_other 1.713 r_angle_refined_deg 1.268 r_angle_other_deg 0.736 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 1766 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing