5T8S | pdb_00005t8s

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IML

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	NegoA.00040.a.B1.PW37902 at 20.8 mg/ml, mixed with 2 mM each ATP, 2 mM L-Met, and 2 mM MgCl2, then mixed 1:1 and incubated with an equal volume Morpheus(f12): 12.5% (w/v) PEG-1000, 12.5 % (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/Trizma base, pH = 8.5, 0.02 M each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.71	α = 90
b = 115.71	β = 90
c = 146.24	γ = 90

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2016-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	50	99.8	0.08	0.999	21.47	12.4		108870		-3	16.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	99.5		0.568	0.936	4.96	12.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3IML	1.7	37.278	106709	1954	97.79	0.1488	0.1484	0.1487	0.1706	0.1697	24.684

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.536
f_angle_d	0.874
f_chiral_restr	0.057
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5715
Nucleic Acid Atoms
Solvent Atoms	691
Heterogen Atoms	81

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.