9QM6 | pdb_00009qm6

Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O7C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Well solution: 26% PEG 400 and 0.1M MgCl2 in 1M MES pH 6.5 Cryoprotection: 30% PEG 400 Protein: 13.5 mg/ml in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM PLP with 5 mM norleucin

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.426	α = 90
b = 86.426	β = 90
c = 862.41	γ = 120

Symmetry
Space Group	P 61 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 EIGER X 16M	Kirkpatrick-Baez pair of bi-morph mirrors	2022-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

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	2.61	143.74	94.7	0.231	0.235	0.038	0.998	14.8	37.9		39975

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	2.61	2.9	74.4		2.982	3.023	0.496	0.623	1.6	36.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.607	37.84	39943	1998	65.7	0.2507	0.2498	0.2332	0.2678	0.2454	RANDOM	84.4

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]
-1.4075			-1.4075		2.815

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.46
t_omega_torsion	2.33
t_angle_deg	0.9
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12263
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	100

Software

Software
Software Name	Purpose
BUSTER	refinement
Coot	model building
PHASER	phasing
XDS	data reduction
STARANISO	data scaling
Aimless	data scaling
autoPROC	data processing

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.