5VKA | pdb_00005vka

Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and N-omega-hydroxy-L-arginine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5V2Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277.15	0.5 ul 72 mg/ml selenomethionine containing EFE (9 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution of 10 mM N-omega-hydroxy-L-arginine, and 0.2 uL of 100 mM 2OG. The sitting drop reservoir of 200 ul contained 20% w/v Polyethylene glycol 6,000, 0.1 M Tris pH 8.0, 0.2 M Lithium chloride. The crystal was soaked for about a minute in 25% w/v ethylene glycol, 75% reservoir solution before freezing it.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.583	α = 90
b = 82.098	β = 90
c = 87.766	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.169	48.58	99.2	0.094	0.103	0.042	0.997	12.3	5.7		118142			9.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.169	1.19	87.9		0.593	0.687	0.339	0.752		3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	5V2Z	1.169	38.701	1.9	111915	5867	97.54	0.1732	0.1724	0.17	0.1876	0.19	16.2119

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	14.283
f_angle_d	0.961
f_chiral_restr	0.076
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2728
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	40

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.