6YRW

SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15PLP 5mM D-serine 100mM Cacodylate 0.1M ph 6.5 Sodium citrate 0.85M
Crystal Properties
Matthews coefficientSolvent content
4.2470.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 199.956α = 90
b = 113.657β = 94.13
c = 132.479γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.9697ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3347.8576.010.9541.891.5980329
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5650.95

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 REPLACEMENTTHROUGHOUT4WXG2.547.8573924383876.010.17880.17630.2265RANDOM40.372
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]
-2.82-3.26-0.133.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg16.246
r_dihedral_angle_3_deg16.187
r_dihedral_angle_1_deg7.208
r_angle_refined_deg1.587
r_angle_other_deg1.286
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg16.246
r_dihedral_angle_3_deg16.187
r_dihedral_angle_1_deg7.208
r_angle_refined_deg1.587
r_angle_other_deg1.286
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12472
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASERphasing