3BT7

Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BH2	PDB entry 2BH2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	295	100 mM sodium cacodylate pH 7.4, 200 mM sodium sulfate, and 22 % PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.407	α = 90
b = 70.131	β = 120.88
c = 107.95	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 315r		2007-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

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	2.43	35.1		0.078	5.7	2.2	90859	42023	2	2

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	2.43	2.49	83.7		0.27	1.7	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	PDB entry 2BH2	2.43	35.07	38764	3230	93.62	0.2297	0.22509	0.28635	RANDOM	47.563

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]
-0.02		-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_3_deg	20.099
r_dihedral_angle_4_deg	15.169
r_dihedral_angle_1_deg	6.715
r_scangle_it	3.392
r_scbond_it	2.102
r_angle_refined_deg	1.781
r_mcangle_it	1.453
r_angle_other_deg	1.434
r_mcbond_it	0.78
r_symmetry_hbond_refined	0.275
r_symmetry_vdw_other	0.25
r_xyhbond_nbd_refined	0.213
r_mcbond_other	0.143
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5914
Nucleic Acid Atoms	804
Solvent Atoms	261
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SOLVE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SCALA	data scaling