Experiment: 8JSU

The crystal structure of TvaE in complex with TvaLP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.1 M Amino acids(0.02 M DL-Glutamic acid monohydrate, 0.02 M DL-Alanine, 0.02 M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine), 0.1 M Buffer System 2 (0.05 M Sodium HEPES, 0.05M MOPS(acid)) pH=7.5, 50% v/v Precipitant Mix4 (12.5% v/v MPD, 12.5% v/v PEG 1000, 12.5% v/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.16	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.224	α = 94.72
b = 52.499	β = 90.55
c = 73.673	γ = 112.55

Symmetry
Space Group	P 1

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 PILATUS3 6M		2022-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.44	42.17	92.3	0.045	14.2	2.1		105078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.44	1.45	91.8		0.468	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.44	40.14	1.96	105078	5265	92.32	0.1739	0.1727	0.1735	0.1969	0.1975

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.614
f_angle_d	0.966
f_chiral_restr	0.075
f_plane_restr	0.016
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5199
Nucleic Acid Atoms
Solvent Atoms	685
Heterogen Atoms	38

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing