8WZ8 | pdb_00008wz8

The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(T67A,Q69A) 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
3.08	60.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.6	α = 90
b = 131.6	β = 90
c = 115.886	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		2023-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97853	SSRF	BL18U1

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	2.583	50	97.64	0.992	22.76	38.31		19107			38.31

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	2.583	2.68			0.938

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	2.583	43.524	18665	969	97.631	0.224	0.2215	0.2052	0.2716	0.2579	46.277

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]
-0.201	-0.101		-0.201		0.652

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.59
r_dihedral_angle_6_deg	16.723
r_lrange_it	10.066
r_lrange_other	10.062
r_scangle_it	8.384
r_scangle_other	8.382
r_mcangle_it	7.182
r_mcangle_other	7.181
r_dihedral_angle_1_deg	6.434
r_scbond_it	5.872
r_scbond_other	5.871
r_dihedral_angle_2_deg	5.747
r_mcbond_it	5.043
r_mcbond_other	5.041
r_angle_refined_deg	1.487
r_angle_other_deg	0.73
r_dihedral_angle_other_2_deg	0.339
r_symmetry_nbd_other	0.232
r_nbd_refined	0.214
r_nbd_other	0.207
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_nbd_refined	0.101
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
r_bond_refined_d	0.01
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	3300
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	49

Software

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