2NZ2 | pdb_00002nz2

Crystal structure of human argininosuccinate synthase in complex with aspartate and citrulline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VL2PDB ENTRY 1VL2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729316% PEG 3350, 0.15M DL-MALIC ACID, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.94α = 90
b = 117.47β = 90
c = 155.15γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2006-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.95373BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.43099.70.1520.2057.3174031735828.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.51000.2680.4553.987.51967

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VL22.419.412216407164078641000.197570.197570.19390.190.264750.25RANDOM17.865
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]
1.050.3-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.051
r_dihedral_angle_3_deg19.682
r_dihedral_angle_4_deg15.73
r_dihedral_angle_1_deg14.546
r_scangle_it2.667
r_angle_refined_deg1.858
r_scbond_it1.726
r_mcangle_it1.108
r_mcbond_it0.669
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.051
r_dihedral_angle_3_deg19.682
r_dihedral_angle_4_deg15.73
r_dihedral_angle_1_deg14.546
r_scangle_it2.667
r_angle_refined_deg1.858
r_scbond_it1.726
r_mcangle_it1.108
r_mcbond_it0.669
r_nbtor_refined0.304
r_symmetry_vdw_refined0.264
r_nbd_refined0.229
r_symmetry_hbond_refined0.223
r_xyhbond_nbd_refined0.195
r_chiral_restr0.162
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms3191
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing