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Crystal Structure of Epithelial Adhesin 9 A domain (Epa9A) 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 0.1 M HEPES PH7, 32% PEG 6000, 0.05 M LACTOSE, VAPOR DIFFUSION IN SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.58 α = 90 b = 66.58 β = 90 c = 117.95 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 CCD MARRESEARCH MX-255 2012-11-16 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 2.15 41.23 99.9 0.1 24.9 10.9 17016 -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 2.15 2.27 100 0.59 4.9 11.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PRUNED VERSION OF PDB ENTRY 4AF9 2.15 41.23 16140 857 99.85 0.1654 0.16391 0.19381 0.1793 RANDOM 27.86
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] 0.03 0.03 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 13.782 r_dihedral_angle_4_deg 9.675 r_dihedral_angle_1_deg 6.957 r_mcangle_it 2.08 r_scbond_it 1.491 r_mcbond_it 1.229 r_angle_refined_deg 1.225 r_mcbond_other 1.225 r_angle_other_deg 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 13.782 r_dihedral_angle_4_deg 9.675 r_dihedral_angle_1_deg 6.957 r_mcangle_it 2.08 r_scbond_it 1.491 r_mcbond_it 1.229 r_angle_refined_deg 1.225 r_mcbond_other 1.225 r_angle_other_deg 0.743 r_chiral_restr 0.074 r_bond_refined_d 0.007 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 1819 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing