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Crystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B8G pdb entry 3B8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.4 291 8% PEG3350, 100 mM ammonium citrate, pH 6.4, EVAPORATION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.802 α = 90 b = 98.802 β = 90 c = 90.107 γ = 120
Symmetry Space Group P 3 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE MAR scanner 300 mm plate 2008-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0 APS 21-ID-D
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 2.21 90.17 96.5 0.07 37.5 10.1 25434 24544
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 2.21 2.29 72.9 0.734 1.3 4.6 1836
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 3B8G 2.21 20 24090 23293 1247 96.69 0.23108 0.22856 0.2276 0.2803 0.2796 RANDOM 45.175
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] -0.38 -0.19 -0.38 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.238 r_dihedral_angle_4_deg 21.493 r_dihedral_angle_3_deg 19.727 r_dihedral_angle_1_deg 6.077 r_scangle_it 3.788 r_scbond_it 2.446 r_angle_refined_deg 1.789 r_mcangle_it 1.469 r_mcbond_it 0.89 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.238 r_dihedral_angle_4_deg 21.493 r_dihedral_angle_3_deg 19.727 r_dihedral_angle_1_deg 6.077 r_scangle_it 3.788 r_scbond_it 2.446 r_angle_refined_deg 1.789 r_mcangle_it 1.469 r_mcbond_it 0.89 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3227 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing