7N63 | pdb_00007n63

X-ray structure of HCAN_0200, an aminotransferase from Helicobacter canadensis in complex with its external aldimine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5U1Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	Enzyme incubated with 1 mM PLP and 5 mM dTDP-3-amino-3,6-dideoxyglucose. Precipitant = 15-18 % PEG 3350, 100 mM MgCl2, 100 mM MES, pH 6.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.005	α = 90
b = 150.766	β = 90
c = 91.058	γ = 90

Symmetry
Space Group	C 2 2 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	Bruker PHOTON II		2021-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.4	50	98.6	0.068	12.7	6		81651

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.5	96.3		0.41	2.7	3.4

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	THROUGHOUT	5u1z	1.4	35.71	77505	4146	98.66	0.172	0.1711	0.1716	0.1897	0.1895	RANDOM	11.104

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
r_dihedral_angle_2_deg	35.642
r_dihedral_angle_4_deg	22.447
r_dihedral_angle_3_deg	11.247
r_dihedral_angle_1_deg	6.445
r_angle_refined_deg	1.782
r_angle_other_deg	1.542
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2919
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	85

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
PHASER	phasing