4IG6 | pdb_00004ig6

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	289	AnphA.00316.a.A1 PS00323 at 21 mg/mL with 3 mM SAH against JCSG+ A4: 30% MPD, 20 mM calcium chloride, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.54	72.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.11	α = 90
b = 105.11	β = 90
c = 92.25	γ = 90

Symmetry
Space Group	P 43 21 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	RIGAKU SATURN 944+	VariMax	2012-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.4	50	99.7	0.082	20.95	7.5	20842	20785		-3	40.675

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	2.4	2.46	99.9		0.536	4.31

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 3KNU	2.4	41.92	20749	1064	99.8	0.1767	0.1752	0.18	0.2037	0.21	RANDOM	35.5847

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]
-0.71			-0.71		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.633
r_dihedral_angle_4_deg	16.671
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	4.942
r_mcangle_it	3.358
r_mcbond_it	1.994
r_mcbond_other	1.994
r_angle_refined_deg	1.422
r_angle_other_deg	0.744
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.633
r_dihedral_angle_4_deg	16.671
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	4.942
r_mcangle_it	3.358
r_mcbond_it	1.994
r_mcbond_other	1.994
r_angle_refined_deg	1.422
r_angle_other_deg	0.744
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1716
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	28

Software

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