8HX6

Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae


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
2.2244.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.67α = 90
b = 171.405β = 90
c = 160.838γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-03MSINGLE 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
12.1447.2799.80.0230.99918.996.87467052.19
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)
12.142.2298.10.5810.641.296.7

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 REPLACEMENTTHROUGHOUT1qdl2.1447.2670936373499.760.226620.224290.27161RANDOM64.996
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]
-1.625.66-4.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.86
r_dihedral_angle_3_deg15.396
r_dihedral_angle_4_deg14.36
r_dihedral_angle_1_deg6.319
r_long_range_B_refined2.693
r_long_range_B_other2.692
r_mcangle_it1.506
r_mcangle_other1.506
r_angle_refined_deg1.197
r_scangle_other1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.86
r_dihedral_angle_3_deg15.396
r_dihedral_angle_4_deg14.36
r_dihedral_angle_1_deg6.319
r_long_range_B_refined2.693
r_long_range_B_other2.692
r_mcangle_it1.506
r_mcangle_other1.506
r_angle_refined_deg1.197
r_scangle_other1.08
r_angle_other_deg1.061
r_mcbond_it0.827
r_mcbond_other0.827
r_scbond_it0.578
r_scbond_other0.578
r_chiral_restr0.038
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms10107
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing