6X0C

Tryptophan Synthase mutant beta-Q114A in complex with Cesium ion at the metal coordination site and aminoacrylate and benzimidazole at the enzyme beta site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VFD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.6253.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.133α = 90
b = 59.336β = 95.11
c = 67.419γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979200APS24-ID-C

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
11.45401000.1040.1040.1110.030.99813.713.3127033
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)
11.451.5399.91.1031.1031.1730.3230.613

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 REPLACEMENTTHROUGHOUT6VFD1.4539.39120752626099.490.16560.16360.202RANDOM27.857
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]
0.680.35-1.050.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.652
r_dihedral_angle_4_deg17.015
r_dihedral_angle_3_deg13.533
r_dihedral_angle_1_deg6.671
r_rigid_bond_restr3.795
r_angle_refined_deg1.57
r_angle_other_deg1.485
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.652
r_dihedral_angle_4_deg17.015
r_dihedral_angle_3_deg13.533
r_dihedral_angle_1_deg6.671
r_rigid_bond_restr3.795
r_angle_refined_deg1.57
r_angle_other_deg1.485
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4894
Nucleic Acid Atoms
Solvent Atoms608
Heterogen Atoms100

Software

Software
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
PHASERphasing
PARROTphasing
REFMACrefinement
PDB_EXTRACTdata extraction