8WZ9 | pdb_00008wz9

The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 in ternary complex with NAD and adenine

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	0.5 M Ammonium sulfate 1.0 M Lithium sulfate 0.1 M Sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.82	α = 90
b = 130.82	β = 90
c = 117.118	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		2023-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97861	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.649	50	100	0.102	0.103	0.017	0.999	50.3	38.6		71306

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	1.649	1.71			0.806

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Q5ZTY7	1.649	25.511	71071	3525	99.651	0.176	0.176	0.1828	0.1816	0.1922	25.143

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]
-0.35	-0.175		-0.35		1.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.621
r_dihedral_angle_3_deg	15.107
r_lrange_it	6.566
r_dihedral_angle_1_deg	6.418
r_lrange_other	6.264
r_scangle_other	5.379
r_scangle_it	5.37
r_dihedral_angle_2_deg	4.314
r_scbond_other	3.676
r_scbond_it	3.669
r_mcangle_it	3.022
r_mcangle_other	3.021
r_mcbond_it	2.236
r_mcbond_other	2.235
r_angle_refined_deg	1.405
r_angle_other_deg	0.681
r_dihedral_angle_other_2_deg	0.327
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.207
r_nbd_other	0.189
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.171
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.068
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	508
Heterogen Atoms	64

Software

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