☰ Navigation Tabs
The crystal structure of Glycoside Hydrolase BglX from P. aeruginosa in complex with 1-deoxynojirimycin
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 50 mM Bis Tris, pH 6.5, 30% pentaerythritol ethoxylate and 50 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.942 α = 90 b = 86.882 β = 90 c = 244.18 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 PIXEL DECTRIS PILATUS 6M 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979310 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 86.88 97.2 0.11 6.8 8.9 109537
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 2.03 0.58
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 81.99 103893 5540 97.04 0.16594 0.16433 0.1745 0.19606 0.205 RANDOM 21.568
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] 2.86 -1.74 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 20.831 r_dihedral_angle_3_deg 13.135 r_dihedral_angle_1_deg 6.938 r_long_range_B_refined 5.987 r_long_range_B_other 5.746 r_scangle_other 4.105 r_scbond_it 2.589 r_scbond_other 2.588 r_mcangle_it 2.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.206 r_dihedral_angle_4_deg 20.831 r_dihedral_angle_3_deg 13.135 r_dihedral_angle_1_deg 6.938 r_long_range_B_refined 5.987 r_long_range_B_other 5.746 r_scangle_other 4.105 r_scbond_it 2.589 r_scbond_other 2.588 r_mcangle_it 2.299 r_mcangle_other 2.299 r_mcbond_it 1.537 r_mcbond_other 1.536 r_angle_refined_deg 1.497 r_angle_other_deg 1.378 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 1206 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing