3MB5 | pdb_00003mb5

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LGA	PDB code 3LGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	2.8M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.55	α = 90
b = 89.26	β = 90
c = 110.32	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC QUANTUM 315r	bi-morph mirrors	2010-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.98	SOLEIL	PROXIMA 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	1.6	20	99.8	0.103	16.42	9.1		56562			22

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)
	1.6	1.7	99.9		0.317	5.1	5.8	9295

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 code 3LGA	1.6	19.7	53652	2824	100	0.18473	0.18397	0.18	0.19891	0.2	RANDOM	25.151

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]
1.84			0.3		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.229
r_dihedral_angle_3_deg	11.611
r_dihedral_angle_4_deg	11.294
r_dihedral_angle_1_deg	6.001
r_scangle_it	4.214
r_scbond_it	2.505
r_mcangle_it	1.538
r_angle_refined_deg	1.373
r_mcbond_it	0.823
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.229
r_dihedral_angle_3_deg	11.611
r_dihedral_angle_4_deg	11.294
r_dihedral_angle_1_deg	6.001
r_scangle_it	4.214
r_scbond_it	2.505
r_mcangle_it	1.538
r_angle_refined_deg	1.373
r_mcbond_it	0.823
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	75

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.