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Crystal structure of NagZ from Neisseria gonorrhoeae in complex with N-acetylglucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JTI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M Sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 pH8.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.184 α = 90 b = 125.307 β = 90 c = 190.614 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 CCD ADSC QUANTUM 315r 2018-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U
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 2.18 104.71 99.9 0.116 14.7 6.7 127747
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 2.18 2.22 98.3 0.67 2.9 6.2
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 6JTI 2.18 104.71 120987 6401 99.67 0.21593 0.21443 0.2191 0.24395 0.2468 RANDOM 35.848
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] -0.2 0.29 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 17.348 r_dihedral_angle_3_deg 13.809 r_long_range_B_refined 6.477 r_long_range_B_other 6.429 r_dihedral_angle_1_deg 6.068 r_scangle_other 4.271 r_mcangle_it 3.652 r_mcangle_other 3.652 r_scbond_it 2.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 17.348 r_dihedral_angle_3_deg 13.809 r_long_range_B_refined 6.477 r_long_range_B_other 6.429 r_dihedral_angle_1_deg 6.068 r_scangle_other 4.271 r_mcangle_it 3.652 r_mcangle_other 3.652 r_scbond_it 2.598 r_scbond_other 2.598 r_mcbond_it 2.283 r_mcbond_other 2.283 r_angle_refined_deg 1.367 r_angle_other_deg 1.238 r_chiral_restr 0.122 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 15608 Nucleic Acid Atoms Solvent Atoms 1062 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing