6X94

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DQ3PDB entry 2DQ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729518% PEG3350, 200 mM thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.7154.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.782α = 90
b = 159.415β = 90
c = 84.004γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979460SSRLBL12-2

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
11.4579.70799.90.060.060.0630.02118.19.986540
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)
11.451.531001.1541.1541.2170.3830.7250.710

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 2DQ31.4529.2282304420699.870.14540.14420.1685RANDOM22.611
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]
0.26-0.750.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.212
r_dihedral_angle_4_deg18.307
r_dihedral_angle_3_deg13.188
r_dihedral_angle_1_deg5.945
r_angle_refined_deg1.937
r_angle_other_deg1.525
r_chiral_restr0.113
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.212
r_dihedral_angle_4_deg18.307
r_dihedral_angle_3_deg13.188
r_dihedral_angle_1_deg5.945
r_angle_refined_deg1.937
r_angle_other_deg1.525
r_chiral_restr0.113
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3279
Nucleic Acid Atoms
Solvent Atoms694
Heterogen Atoms71

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction