2R8V

Native structure of N-acetylglutamate synthase from Neisseria gonorrhoeae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829125% PEG3350, 100mM CsCl, 100 MM sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5651.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.661α = 90
b = 98.661β = 90
c = 89.755γ = 120
Symmetry
Space GroupP 3 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 4mirrors2007-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.000APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.52099.10.09730.610.91745417297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5998.80.58428.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.5201639687298.940.194380.191530.25234RANDOM27.591
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]
1.760.881.76-2.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.201
r_dihedral_angle_3_deg20.874
r_dihedral_angle_4_deg19.592
r_scangle_it8.66
r_dihedral_angle_1_deg7.672
r_scbond_it6.513
r_mcangle_it3.709
r_mcbond_it2.893
r_angle_refined_deg2.041
r_nbtor_refined0.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.201
r_dihedral_angle_3_deg20.874
r_dihedral_angle_4_deg19.592
r_scangle_it8.66
r_dihedral_angle_1_deg7.672
r_scbond_it6.513
r_mcangle_it3.709
r_mcbond_it2.893
r_angle_refined_deg2.041
r_nbtor_refined0.337
r_symmetry_vdw_refined0.334
r_symmetry_hbond_refined0.317
r_nbd_refined0.304
r_xyhbond_nbd_refined0.217
r_chiral_restr0.146
r_gen_planes_refined0.02
r_bond_refined_d0.011
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 AtomsNumber
Protein Atoms3227
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
CNSrefinement