4H3Y | pdb_00004h3y

Crystal structure of an asymmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in one half-site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AXZ	PDB ENTRY 3axz

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	BuphA.00054.a.A1 PS01368 at 35.3 mg/mL against JCSG II screen condition F12, 0.1 M phosphate-citrate pH 4.2, 5% PEG 3000, 25% 1,2 propanediol, 10% glycerol, crystal tracking ID 230666f12, unique puck ID zjg9-5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 187.4	β = 90
c = 127.64	γ = 90

Symmetry
Space Group	C 2 2 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		2012-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.000	ALS	5.0.2

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	2.5	50	99.4	0.06	26.05	7.2	24981	24828		-3	51.36

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	2.5	2.57	99.6		0.544	4.12

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3axz	2.5	19.87	24828	1266	99.37	0.184	0.1813	0.19	0.2324	0.23	RANDOM	49.7717

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]
1.83			-0.9		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.873
r_dihedral_angle_4_deg	19.204
r_dihedral_angle_3_deg	15.242
r_dihedral_angle_1_deg	6.117
r_angle_refined_deg	1.465
r_angle_other_deg	0.83
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.873
r_dihedral_angle_4_deg	19.204
r_dihedral_angle_3_deg	15.242
r_dihedral_angle_1_deg	6.117
r_angle_refined_deg	1.465
r_angle_other_deg	0.83
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3855
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	27

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	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.