6AM9

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser-bound in a predominantly closed state.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VM5 

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
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.502α = 90
b = 109.122β = 90
c = 160.491γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-03MSINGLE 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
12.094099.60.030.99813.56.791166
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)
12.092.1399.70.7390.6956.9

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 REPLACEMENTTHROUGHOUT5VM52.094086509452499.420.2160.214490.24397RANDOM60.15
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]
2.91-2.34-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.916
r_dihedral_angle_4_deg14.383
r_dihedral_angle_3_deg13.183
r_dihedral_angle_1_deg5.722
r_long_range_B_refined4.179
r_long_range_B_other4.176
r_angle_refined_deg1.21
r_angle_other_deg0.898
r_mcangle_it0.778
r_mcangle_other0.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.916
r_dihedral_angle_4_deg14.383
r_dihedral_angle_3_deg13.183
r_dihedral_angle_1_deg5.722
r_long_range_B_refined4.179
r_long_range_B_other4.176
r_angle_refined_deg1.21
r_angle_other_deg0.898
r_mcangle_it0.778
r_mcangle_other0.778
r_scangle_other0.611
r_mcbond_it0.443
r_mcbond_other0.441
r_scbond_it0.345
r_scbond_other0.342
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms11369
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing