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The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with lactose
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 2.23 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.978 α = 65.55 b = 73.588 β = 73.42 c = 81.124 γ = 69.68
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 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 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 1.6 45.17 96.1 0.05 10.8 3.3 175334
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 1.6 1.63 0.51
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 1.6 45.17 166499 8830 96.12 0.14082 0.13935 0.1528 0.1684 0.1776 RANDOM 20.863
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] 0.31 0.13 -1.1 -0.44 0.98 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_4_deg 19.985 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_1_deg 6.779 r_long_range_B_refined 6.524 r_long_range_B_other 6.523 r_scangle_other 4.888 r_scbond_it 3.207 r_scbond_other 3.206 r_mcangle_it 2.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_4_deg 19.985 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_1_deg 6.779 r_long_range_B_refined 6.524 r_long_range_B_other 6.523 r_scangle_other 4.888 r_scbond_it 3.207 r_scbond_other 3.206 r_mcangle_it 2.471 r_mcangle_other 2.471 r_angle_refined_deg 1.81 r_mcbond_it 1.787 r_mcbond_other 1.786 r_angle_other_deg 1.594 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 11274 Nucleic Acid Atoms Solvent Atoms 1392 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing