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Crysta structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and N-acetyl-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 291 6% PEG3350, 100mM CsCl, 100 mM sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.65 α = 90 b = 98.65 β = 90 c = 89.754 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 298 IMAGE PLATE RIGAKU RAXIS IV mirrors 2007-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 2.6 20 99.2 0.095 13.2 8 15619 15494
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 2.6 2.69 96.9 0.927 1.5 5.8
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 2R8V 2.6 20 15494 14685 773 98.91 0.20392 0.19998 0.2003 0.28239 0.2232 RANDOM 35.11
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] 0.62 0.31 0.62 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.47 r_dihedral_angle_3_deg 23.069 r_dihedral_angle_4_deg 22.803 r_scangle_it 9.848 r_dihedral_angle_1_deg 8.554 r_scbond_it 6.862 r_mcangle_it 3.986 r_mcbond_it 2.545 r_angle_refined_deg 2.407 r_symmetry_vdw_refined 0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.47 r_dihedral_angle_3_deg 23.069 r_dihedral_angle_4_deg 22.803 r_scangle_it 9.848 r_dihedral_angle_1_deg 8.554 r_scbond_it 6.862 r_mcangle_it 3.986 r_mcbond_it 2.545 r_angle_refined_deg 2.407 r_symmetry_vdw_refined 0.351 r_nbtor_refined 0.35 r_nbd_refined 0.317 r_symmetry_hbond_refined 0.316 r_xyhbond_nbd_refined 0.228 r_chiral_restr 0.163 r_gen_planes_refined 0.024 r_bond_refined_d 0.012 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 3227 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing CNS refinement