3CEP

Structure of a tryptophan synthase quinonoid intermediate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829350mM bicine (pH 7.8), 1mM EDTA, 5mM dithioerythritol, 0.02mM pyridoxal phosphate solution, 2mM spermine, and 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.024α = 90
b = 58.908β = 95.19
c = 67.086γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210double-crystal monochromator Si(111), beam focused by a toroidal mirror2001-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.12497.90.1196.72.54112841128-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2980.3483.12.55293

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1QOP2.123.7391103911020171000.199970.199970.197980.23843RANDOM21.75
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]
-2.21-0.023.09-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.185
r_dihedral_angle_4_deg15.804
r_dihedral_angle_3_deg13.368
r_dihedral_angle_1_deg5.526
r_scangle_it2.014
r_scbond_it1.189
r_angle_refined_deg1.158
r_mcangle_it0.734
r_mcbond_it0.385
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.185
r_dihedral_angle_4_deg15.804
r_dihedral_angle_3_deg13.368
r_dihedral_angle_1_deg5.526
r_scangle_it2.014
r_scbond_it1.189
r_angle_refined_deg1.158
r_mcangle_it0.734
r_mcbond_it0.385
r_nbtor_refined0.299
r_metal_ion_refined0.222
r_nbd_refined0.193
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.128
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4936
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing