8HX9

Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae 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
2.2445.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.289α = 90
b = 170.784β = 90
c = 162.079γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-23MSINGLE 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
12.0347.4899.90.022120.877.68886745.02
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)
12.032.199.80.61811.417.2

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 REPLACEMENTTHROUGHOUT1QDL2.0347.4784467444699.870.220770.217710.2794RANDOM63.689
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]
-1.18.03-6.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.538
r_dihedral_angle_1_deg6.387
r_long_range_B_refined3.982
r_long_range_B_other3.978
r_dihedral_angle_2_deg3.448
r_mcangle_it3.125
r_mcangle_other3.125
r_scangle_other2.724
r_mcbond_it2.177
r_mcbond_other2.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.538
r_dihedral_angle_1_deg6.387
r_long_range_B_refined3.982
r_long_range_B_other3.978
r_dihedral_angle_2_deg3.448
r_mcangle_it3.125
r_mcangle_other3.125
r_scangle_other2.724
r_mcbond_it2.177
r_mcbond_other2.176
r_scbond_it1.973
r_scbond_other1.973
r_rigid_bond_restr1.076
r_angle_refined_deg0.785
r_angle_other_deg0.282
r_chiral_restr0.039
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10017
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing