6D0V

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CLLPDB entry 2CLL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850 mM bicine-CsOH, 8-10% PEG8000, 2-6 mM spermine, 1 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.73α = 90
b = 60.88β = 94.87
c = 67.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HF2017-11-26MSINGLE 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 Sym I (Observed)Rrim I (All)Rpim I (All)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
11.6491.533900.0560.0790.04110.53.68146481464
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)
11.641.7383.60.2130.2130.2960.1523.13.6

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 2CLL1.6437.3277328404489.570.13180.12950.175RANDOM21.925
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]
-0.730.221.72-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.339
r_sphericity_free22.944
r_dihedral_angle_4_deg16.807
r_dihedral_angle_3_deg12.006
r_sphericity_bonded10.634
r_dihedral_angle_1_deg6.288
r_rigid_bond_restr2.395
r_angle_refined_deg1.516
r_chiral_restr0.103
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.339
r_sphericity_free22.944
r_dihedral_angle_4_deg16.807
r_dihedral_angle_3_deg12.006
r_sphericity_bonded10.634
r_dihedral_angle_1_deg6.288
r_rigid_bond_restr2.395
r_angle_refined_deg1.516
r_chiral_restr0.103
r_bond_refined_d0.009
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4996
Nucleic Acid Atoms
Solvent Atoms794
Heterogen Atoms169

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
DMphasing
PDB_EXTRACTdata extraction