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Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Crystallographic structure of NagZ from Pseudomonas aeruginosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 30% PEG 8000,
100 mM Sodium Cacodylate pH 6.0,
200 mM Sodium Acetate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.14 α = 90 b = 66.93 β = 98.57 c = 74.06 γ = 90
Symmetry Space Group P 1 21 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 2015-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97925 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 3.1 73.23 93.1 0.182 0.146 0.929 4.2 2.2 10753 2 19.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 92.7 0.405 0.75 2.2 2.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Crystallographic structure of NagZ from Pseudomonas aeruginosa 3.1 73.23 10175 565 92.67 0.22069 0.21684 0.213 0.2909 0.2861 RANDOM 17.773
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] 4.29 1.53 -2.99 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.473 r_scbond_it 32.705 r_scbond_other 32.692 r_scangle_other 29.748 r_long_range_B_refined 28.006 r_long_range_B_other 28.006 r_mcbond_it 22.072 r_mcbond_other 21.995 r_mcangle_other 21.059 r_mcangle_it 21.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.473 r_scbond_it 32.705 r_scbond_other 32.692 r_scangle_other 29.748 r_long_range_B_refined 28.006 r_long_range_B_other 28.006 r_mcbond_it 22.072 r_mcbond_other 21.995 r_mcangle_other 21.059 r_mcangle_it 21.026 r_dihedral_angle_3_deg 16.196 r_dihedral_angle_4_deg 10.978 r_dihedral_angle_1_deg 6.051 r_angle_other_deg 1.963 r_angle_refined_deg 1.509 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.003 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 5082 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing