6C73

Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HT3PDB entry 4HT3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8298100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 1 mM DTT, 1 mM EDTA, 2 mM F9F
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.609α = 90
b = 58.98β = 94.4
c = 67.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax2017-11-07MSINGLE 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
11.652099.90.0410.0410.0620.0320.99815.13.58520611.917
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)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7499.60.180.180.2530.1350.9613.93.4

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 4HT31.6519.8280889430699.850.14060.13830.1829RANDOM18.708
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]
-0.01-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_sphericity_free27.937
r_dihedral_angle_4_deg17.409
r_dihedral_angle_3_deg12.475
r_sphericity_bonded9.064
r_dihedral_angle_1_deg5.75
r_rigid_bond_restr2.373
r_angle_refined_deg1.535
r_chiral_restr0.102
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_sphericity_free27.937
r_dihedral_angle_4_deg17.409
r_dihedral_angle_3_deg12.475
r_sphericity_bonded9.064
r_dihedral_angle_1_deg5.75
r_rigid_bond_restr2.373
r_angle_refined_deg1.535
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5005
Nucleic Acid Atoms
Solvent Atoms917
Heterogen Atoms150

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction