7KQ9

The aminoacrylate form of the beta-Q114A mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.629850 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 7.6
Crystal Properties
Matthews coefficientSolvent content
2.330.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.622α = 90
b = 59.92β = 94.87
c = 67.416γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-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)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
11.49990.98298.40.0690.0690.080.03110.16.6114154
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)
11.51.5897.60.4780.4780.5590.221.36.3

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 REPLACEMENTTHROUGHOUT6VFD1.539.28107867576897.80.17960.17760.2166RANDOM39.64
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]
-0.98-0.211.15-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.009
r_dihedral_angle_4_deg18.649
r_dihedral_angle_3_deg13.369
r_rigid_bond_restr9.45
r_dihedral_angle_1_deg6.258
r_angle_refined_deg1.537
r_chiral_restr0.103
r_gen_planes_refined0.009
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4852
Nucleic Acid Atoms
Solvent Atoms616
Heterogen Atoms96

Software

Software
Software NamePurpose
xia2data reduction
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction