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Crystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R8V pdb entry 2R8V
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 3.12 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.054 α = 90 b = 107.054 β = 90 c = 185.466 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 2.56 185.7 91.2 0.115 13.2 3.5 39196 35747
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 2.56 2.63 86.4 0.701 1.5 2.6 3330
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2R8V 2.56 20 0.359 37231 33955 1786 90.76 0.21667 0.21378 0.212 0.27252 0.2701 RANDOM 29.582
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] -0.24 -0.12 -0.24 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.278 r_dihedral_angle_3_deg 20.783 r_dihedral_angle_4_deg 20.171 r_dihedral_angle_1_deg 6.635 r_scangle_it 3.257 r_scbond_it 2.056 r_angle_refined_deg 1.8 r_mcangle_it 1.11 r_mcbond_it 0.628 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.278 r_dihedral_angle_3_deg 20.783 r_dihedral_angle_4_deg 20.171 r_dihedral_angle_1_deg 6.635 r_scangle_it 3.257 r_scbond_it 2.056 r_angle_refined_deg 1.8 r_mcangle_it 1.11 r_mcbond_it 0.628 r_nbtor_refined 0.321 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6446 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing