6TI1

SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/L-Threonine/Lys230 gem diamine complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WXG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15PLP 0.1M D-Threonine 100mM Cacodylate 0.1 ph 6.5 Sodium citrate 1M
Crystal Properties
Matthews coefficientSolvent content
3.5164.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.708α = 90
b = 114.708β = 90
c = 192.063γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9798ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1298.4899.980.0610.33.687017
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0580.06

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4WXG298.488701799.980.17780.177845.696
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.081
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg15.146
r_dihedral_angle_1_deg6.75
r_angle_refined_deg1.863
r_angle_other_deg1.495
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.081
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg15.146
r_dihedral_angle_1_deg6.75
r_angle_refined_deg1.863
r_angle_other_deg1.495
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6236
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASERphasing