4G67

Crystal structure of a COG1565 superfamily member and likely methyl transferase from Burkholderia thailandensis bound to S-adenosyl-homocysteine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	289	ButhA.17973.a.A1 PS01383 at 20 mg/mL with 2 mM SAH against JCSG+ H7 focus screen, 0.2 M ammonium sulfate, 0.1 M BisTris, 18% PEG 3350 and 15% ethylene glycol as cryo-protectant, crystal tracking ID 234263h3, unique puck ID xgv5-2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.63	α = 90
b = 74.55	β = 90
c = 111.79	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	ADSC QUANTUM 315r		2012-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8		99	0.098	13.31			35828		-3	21.529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	91.2		0.522	2.54

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	44.76	35827	1783	99.04	0.1605	0.1586	0.1982	RANDOM	16.5289

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]
-0.56			-1.01		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.395
r_dihedral_angle_4_deg	15.218
r_dihedral_angle_3_deg	12.419
r_dihedral_angle_1_deg	5.621
r_angle_refined_deg	1.521
r_angle_other_deg	0.818
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.395
r_dihedral_angle_4_deg	15.218
r_dihedral_angle_3_deg	12.419
r_dihedral_angle_1_deg	5.621
r_angle_refined_deg	1.521
r_angle_other_deg	0.818
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2869
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.