6AMC

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DVZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.85	298	15-25% PEG3350 and 0.1 M Na HEPES pH 7.85

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.34

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.93	40	99.7	0.023	0.998	15.4	6.7		114421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.96	99.6		0.547	0.605	1.3	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5DVZ	1.93	40	108623	5711	99.54	0.218	0.21604	0.25527	RANDOM	50.408

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]
-0.11			2.95		-2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.823
r_dihedral_angle_4_deg	18.024
r_dihedral_angle_3_deg	13.777
r_dihedral_angle_1_deg	4.908
r_long_range_B_refined	4.403
r_long_range_B_other	4.392
r_angle_refined_deg	1.241
r_angle_other_deg	0.879
r_mcangle_it	0.789
r_mcangle_other	0.788
r_scangle_other	0.583
r_mcbond_it	0.444
r_mcbond_other	0.444
r_scbond_it	0.32
r_scbond_other	0.319
r_chiral_restr	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	11501
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing