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Crystal structure of native NagZ from Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M Sodium acetate trihydrate, 20% w/v Polyethylene glycol 3,350 pH8.0
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.017 α = 90 b = 124.088 β = 90 c = 189.92 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 2017-03-10 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 2.2 103.88 100 0.102 19.7 14.1 122838
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 2.2 2.26 99.9 0.656 9.4
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 4G6C 2.2 103.88 116558 6172 99.92 0.2151 0.21416 0.2176 0.23254 0.2369 RANDOM 41.63
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] -1.13 1.43 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.462 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 13.333 r_long_range_B_other 6.37 r_long_range_B_refined 6.367 r_dihedral_angle_1_deg 6.256 r_scangle_other 4.439 r_mcangle_it 4 r_mcangle_other 4 r_scbond_it 2.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.462 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 13.333 r_long_range_B_other 6.37 r_long_range_B_refined 6.367 r_dihedral_angle_1_deg 6.256 r_scangle_other 4.439 r_mcangle_it 4 r_mcangle_other 4 r_scbond_it 2.658 r_scbond_other 2.658 r_mcbond_it 2.509 r_mcbond_other 2.508 r_angle_refined_deg 1.476 r_angle_other_deg 0.988 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 15667 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection HKL-3000 data scaling PHENIX phasing REFMAC refinement