8WZ7 | pdb_00008wz7

The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(I255A,T287A) in ternary complex with NAD and adenosine

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	0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.657	α = 90
b = 130.657	β = 90
c = 113.834	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	1.92	50	99.68	0.944	3.9	38.5		44078			28.04

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	1.922	1.991			0.856

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	1.922	37.945	43919	2145	99.685	0.206	0.2055	0.2088	0.2252	0.229	28.875

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]
					-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.627
r_dihedral_angle_3_deg	15.248
r_lrange_it	7.311
r_lrange_other	7.31
r_dihedral_angle_1_deg	6.483
r_scangle_it	6.15
r_scangle_other	6.149
r_scbond_it	4.481
r_scbond_other	4.479
r_dihedral_angle_2_deg	4.343
r_mcangle_it	3.976
r_mcangle_other	3.976
r_mcbond_it	3.228
r_mcbond_other	3.228
r_angle_refined_deg	1.406
r_angle_other_deg	0.681
r_dihedral_angle_other_2_deg	0.268
r_nbd_refined	0.214
r_symmetry_nbd_other	0.212
r_nbd_other	0.202
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_refined	0.17
r_symmetry_nbd_refined	0.104
r_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.07
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	3301
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	63

Software

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