6IJE | pdb_00006ije

Crystal structure of the type VI amidase immunity (Tai4) from Agrobacterium tumefaciens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZFI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	33 % PEG 6000, 1.5 M lithium chloride, 100 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.921	α = 90
b = 57.756	β = 90
c = 71.465	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 PILATUS3 6M		2015-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	53.92	99.5	0.067	0.073	0.029	0.998	13	6.2		32919

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	94.7		0.568	0.654	0.313	0.807		4.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ZFI	1.55	44.96	31307	1556	99.33	0.1753	0.1742	0.1858	0.1975	0.2059	RANDOM	25.599

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]
0.03			1.55		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.301
r_dihedral_angle_4_deg	17.569
r_dihedral_angle_3_deg	16.993
r_dihedral_angle_1_deg	5.814
r_angle_refined_deg	1.794
r_angle_other_deg	1.602
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1498
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	28

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
MOLREP	phasing