8WWG | pdb_00008wwg

The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 complex with NAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other		Q5ZTY7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	2.0 M Ammonium sulfate 0.1 M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.467	α = 90
b = 130.467	β = 90
c = 115.523	γ = 120

Symmetry
Space Group	P 62 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		2023-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97923	SSRF	BL19U1

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	1.921	42.805	99.45	0.981	56.33	38.4		1710554			38.7

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	1.921	1.99			0.802

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	1.921	42.705	44469	2193	99.595	0.21	0.2095	0.2063	0.2204	0.228	40.573

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]
-0.005	-0.003		-0.005		0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.789
r_dihedral_angle_3_deg	16.789
r_lrange_it	7.387
r_lrange_other	7.387
r_dihedral_angle_1_deg	6.517
r_scangle_it	6.51
r_scangle_other	6.508
r_scbond_it	4.782
r_scbond_other	4.78
r_mcangle_it	4.414
r_mcangle_other	4.414
r_dihedral_angle_2_deg	4.377
r_mcbond_it	3.797
r_mcbond_other	3.795
r_angle_refined_deg	1.404
r_angle_other_deg	0.684
r_dihedral_angle_other_2_deg	0.27
r_nbd_refined	0.212
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_other	0.207
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.176
r_symmetry_nbd_refined	0.149
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.015
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	3306
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	49

Software

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