6O1H

Tryptophan synthase Q114A mutant in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HPJPDB entry 4HPJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8293100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 2 mM F9F, 0.01 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.6253.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.749α = 90
b = 60.72β = 94.63
c = 67.21γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax Confocal Max-Flux2018-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)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
11.644099.90.0510.0510.060.0310.99911.53.59036916.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.7399.50.3060.3060.3640.1952.43.4

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 REPLACEMENTTHROUGHOUTPDB entry 4HPJ1.6439.3185508444899.420.1560.15380.199RANDOM29.599
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]
0.880.14-0.81-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.805
r_dihedral_angle_4_deg15.609
r_dihedral_angle_3_deg12.593
r_rigid_bond_restr7.957
r_dihedral_angle_1_deg6.309
r_angle_refined_deg1.24
r_chiral_restr0.094
r_bond_refined_d0.006
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4950
Nucleic Acid Atoms
Solvent Atoms743
Heterogen Atoms119

Software

Software
Software NamePurpose
CrystalCleardata collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction