6AMC

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DVZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8529815-25% PEG3350 and 0.1 M Na HEPES pH 7.85
Crystal Properties
Matthews coefficientSolvent content
2.1743.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.438α = 90
b = 110.729β = 90
c = 160.427γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.934099.70.0230.99815.46.7114421
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.9699.60.5470.6051.36.5

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 REPLACEMENTTHROUGHOUT5DVZ1.9340108623571199.540.2180.216040.25527RANDOM50.408
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]
-0.112.95-2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg18.024
r_dihedral_angle_3_deg13.777
r_dihedral_angle_1_deg4.908
r_long_range_B_refined4.403
r_long_range_B_other4.392
r_angle_refined_deg1.241
r_angle_other_deg0.879
r_mcangle_it0.789
r_mcangle_other0.788
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg18.024
r_dihedral_angle_3_deg13.777
r_dihedral_angle_1_deg4.908
r_long_range_B_refined4.403
r_long_range_B_other4.392
r_angle_refined_deg1.241
r_angle_other_deg0.879
r_mcangle_it0.789
r_mcangle_other0.788
r_scangle_other0.583
r_mcbond_it0.444
r_mcbond_other0.444
r_scbond_it0.32
r_scbond_other0.319
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11501
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing