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Crystal Structure of Epithelial Adhesin 9 A domain (Epa9A) from Candida glabrata in complex with Galb1-4GlcNAc
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 0.1 M MAGNESIUM CHLORIDE, 0.1M SODIUM CHLORIDE, 0.1 M MES PH6.5, 12% PEG 4000, 0.05 M LACTOSE, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALB1-4GLCNAC
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.84 α = 90 b = 66.84 β = 90 c = 115.95 γ = 120
Symmetry Space Group P 31 2 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 2013-02-13 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 2.58 40.96 99.9 0.12 15.7 8.1 9889 -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 2.58 2.72 100 0.58 3.7 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 2.6 41 9180 492 99.86 0.18392 0.18086 0.185 0.24228 0.2515 RANDOM 36.072
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] -0.13 -0.13 -0.13 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_4_deg 14.284 r_dihedral_angle_1_deg 7.057 r_mcangle_it 1.972 r_angle_refined_deg 1.312 r_mcbond_it 1.101 r_mcbond_other 1.101 r_scbond_it 1.087 r_angle_other_deg 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_4_deg 14.284 r_dihedral_angle_1_deg 7.057 r_mcangle_it 1.972 r_angle_refined_deg 1.312 r_mcbond_it 1.101 r_mcbond_other 1.101 r_scbond_it 1.087 r_angle_other_deg 0.762 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing