8WKJ | pdb_00008wkj

The crystal structure of aspartate aminotransferases Lpg0070 from Legionella pneumophila

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		Aminotransferase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.1 M Ammonium sulfate 0.05 M Magnesium sulfate heptahydrate 0.1 M Sodium citrate 5.5 22.5 % v/v PEG Smear Medium

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.425	α = 90
b = 105.425	β = 90
c = 165.471	γ = 90

Symmetry
Space Group	I 41 2 2

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		2023-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.978	SSRF	BL18U1

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	1.7	50	99	0.135	0.138	0.028	0.996	6.2	24.1		51188			23.29

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	1.7	1.76	90.7		1.373	1.411	0.311	0.707		19.2

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	48.92	50925	2584	99.045	0.156	0.1554	0.1717	23.945

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]
-0.016			-0.016		0.032

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.807
r_dihedral_angle_6_deg	17.997
r_dihedral_angle_3_deg	14.93
r_lrange_it	7.891
r_lrange_other	7.627
r_scangle_it	6.651
r_scangle_other	6.649
r_dihedral_angle_1_deg	5.862
r_scbond_other	4.513
r_scbond_it	4.509
r_mcangle_it	3.819
r_mcangle_other	3.818
r_mcbond_it	2.763
r_mcbond_other	2.763
r_angle_refined_deg	1.426
r_angle_other_deg	0.705
r_nbd_other	0.313
r_nbd_refined	0.215
r_symmetry_nbd_other	0.208
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3004
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing