8WOU | pdb_00008wou

The crystal structure of aspartate aminotransferases Lpg0070 from Legionella pneumophila

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		AF-Q5ZZE1-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M Sodium sulfate 20% w/v PEG 3350 10% v/v Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.16	α = 90
b = 201.02	β = 90
c = 151.49	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	DECTRIS EIGER X 16M		2023-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.987	SSRF	BL10U2

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	2.14	75.86	99.9	0.991	8.4	12.3		55245			45.06

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	2.14	2.2	100		0.579	1.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.14	75.86	55179	2715	99.751	0.238	0.2357	0.24	0.2816	0.29	53.81

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]
4.673			-4		-0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.931
r_dihedral_angle_6_deg	18.137
r_lrange_other	10.567
r_lrange_it	10.563
r_scangle_it	9.309
r_scangle_other	9.299
r_mcangle_it	7.203
r_mcangle_other	7.202
r_scbond_it	6.51
r_scbond_other	6.494
r_dihedral_angle_1_deg	6.252
r_mcbond_it	5.386
r_mcbond_other	5.385
r_angle_refined_deg	1.496
r_angle_other_deg	0.741
r_dihedral_angle_2_deg	0.59
r_symmetry_nbd_other	0.233
r_nbd_other	0.219
r_nbd_refined	0.217
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.085
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.08
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6022
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	20

Software

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