4B17 | pdb_00004b17

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in complex with S-adenosylmethionine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ATN	PDB ENTRY 4ATN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350, 3.0% DEXTRAN SULFATE SODIUM SALT

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.26	α = 90
b = 92.26	β = 90
c = 83.56	γ = 120

Symmetry
Space Group	P 31 2 1

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	MARRESEARCH MAR165	MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL	2012-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	2.6	28.87	99.8	0.1	16.37	7.4		12983		2	30.97

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	2.6	2.7	99.9		0.64	3.27	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 4ATN	2.6	28.874	2	12971	650	99.83	0.1627	0.1609	0.16	0.1961	0.2	28.77

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]
-2.0593			-2.0593		4.1186

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.577
f_angle_d	1.137
f_chiral_restr	0.071
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2880
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	103

Software

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

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.