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The crystal structure the Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with two glucose molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TF0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 100 mM Bis Tris, pH 5.5, 17% PEG 10000 and 100 mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.505 α = 65.64 b = 74.907 β = 74.18 c = 82.102 γ = 68.9
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 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979150 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.4 46.72 84.1 0.07 5.9 2.6 48392
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.48 0.33
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 5TF0 2.4 46.72 46350 1960 83.92 0.23932 0.2378 0.2423 0.27594 0.2843 RANDOM 49.315
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] 10.46 2.8 -3.81 -4.21 0.48 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.297 r_dihedral_angle_4_deg 17.377 r_dihedral_angle_3_deg 16.963 r_long_range_B_refined 8.625 r_long_range_B_other 8.585 r_dihedral_angle_1_deg 7.168 r_mcangle_it 5.158 r_mcangle_other 5.158 r_scangle_other 4.879 r_mcbond_it 3.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.297 r_dihedral_angle_4_deg 17.377 r_dihedral_angle_3_deg 16.963 r_long_range_B_refined 8.625 r_long_range_B_other 8.585 r_dihedral_angle_1_deg 7.168 r_mcangle_it 5.158 r_mcangle_other 5.158 r_scangle_other 4.879 r_mcbond_it 3.308 r_mcbond_other 3.307 r_scbond_it 2.966 r_scbond_other 2.966 r_angle_refined_deg 1.458 r_angle_other_deg 1.138 r_chiral_restr 0.057 r_bond_refined_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11222 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing