7PZT | pdb_00007pzt

Structure of the bacterial toxin, TecA, an asparagine deamidase from Alcaligenes faecalis.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.06 M divalents (0.3 M MgCl2.6H2O + 0.3 M CaCl2.2H2O), 0.1 M buffer system 1 (1.0 M Imidazole, 1.0 M MES monohydrate) pH 6.5, 30 % v/v precipitant mix 1 (40 % v/v PEG 500 MME, 20 % w/v PEG 20000)

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.051	α = 90
b = 71.407	β = 90
c = 95.923	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 EIGER2 X 16M		2019-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97106	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.84	57.31	100	0.989	7.5	6.9		28829

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.87			0.681

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.84	57.344	28759	1428	99.882	0.192	0.1903	0.2	0.2327	0.24	29.58

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]
-1.43			-0.82		2.251

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.266
r_dihedral_angle_4_deg	19.521
r_dihedral_angle_3_deg	14.007
r_dihedral_angle_1_deg	6.581
r_lrange_it	4.746
r_lrange_other	4.746
r_scangle_it	3.666
r_scangle_other	3.665
r_scbond_it	2.616
r_scbond_other	2.552
r_mcangle_it	2.007
r_mcangle_other	2.007
r_mcbond_other	1.614
r_mcbond_it	1.613
r_angle_refined_deg	1.499
r_angle_other_deg	1.356
r_nbd_other	0.222
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.193
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2490
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
CRANK2	phasing