8HX8

Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with chorismate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherPDB 1QDL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729351% (v/v) Tacsimate, 0.1 M Bis-tris propane (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.2344.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.334α = 90
b = 172.848β = 90
c = 161.054γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
12.5547.5199.90.033117.746.94518271.85
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6499.90.8790.581.03

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QDL2.5547.542924226099.850.208740.205680.26799RANDOM91.698
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]
0.428.41-8.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.215
r_dihedral_angle_1_deg6.783
r_long_range_B_refined5.004
r_long_range_B_other5.004
r_dihedral_angle_2_deg3.83
r_mcangle_it3.391
r_mcangle_other3.391
r_scangle_other3.061
r_mcbond_it2.073
r_mcbond_other2.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.215
r_dihedral_angle_1_deg6.783
r_long_range_B_refined5.004
r_long_range_B_other5.004
r_dihedral_angle_2_deg3.83
r_mcangle_it3.391
r_mcangle_other3.391
r_scangle_other3.061
r_mcbond_it2.073
r_mcbond_other2.073
r_scbond_it1.844
r_scbond_other1.844
r_angle_refined_deg0.84
r_angle_other_deg0.301
r_chiral_restr0.039
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms10275
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing