5US8 | pdb_00005us8

2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K92 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein: 10.6 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg; Screen: Classics II (G8), 0.2M Ammonium acetate, 0.1 HEPES (pH 7.5), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.453α = 90
b = 94.453β = 90
c = 188.49γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)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
12.153099.90.0770.0770.03123.37.351703-344.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.191000.7590.7590.2980.792.77.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1K922.1529.4649016251999.910.158120.156050.160.200320.21RANDOM52.267
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]
-0.08-0.04-0.080.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg10.281
r_long_range_B_refined6.283
r_long_range_B_other6.219
r_scangle_other3.512
r_mcangle_other2.96
r_mcangle_it2.959
r_dihedral_angle_1_deg2.854
r_scbond_it2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg10.281
r_long_range_B_refined6.283
r_long_range_B_other6.219
r_scangle_other3.512
r_mcangle_other2.96
r_mcangle_it2.959
r_dihedral_angle_1_deg2.854
r_scbond_it2.28
r_scbond_other2.28
r_mcbond_it1.913
r_mcbond_other1.912
r_angle_refined_deg1.381
r_angle_other_deg0.893
r_chiral_restr0.085
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.009
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6934
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing