7EDC

Crystal structure of mutant tRNA [Gm18] methyltransferase TrmH (E107G) in complex with S-adenosyl-L-methionine from Escherichia coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	PEG6000, HEPES, MPD

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.791	α = 90
b = 60.942	β = 122.965
c = 67.906	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 315		2014-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.00	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.946	50	99.9	0.044	0.96	41.9	3.7		21319

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.9		0.734

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.946	30.977	21319	1110	99.436	0.204	0.2024	0.2421	45.254

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]
-0.004		-0.004	0.006		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.691
r_dihedral_angle_4_deg	20.041
r_dihedral_angle_3_deg	16.94
r_lrange_other	9.048
r_lrange_it	9.038
r_dihedral_angle_1_deg	7.903
r_scangle_it	7.331
r_scangle_other	7.29
r_scbond_it	5.208
r_mcangle_it	5.192
r_mcangle_other	5.191
r_scbond_other	5.133
r_mcbond_it	4.159
r_mcbond_other	4.088
r_angle_refined_deg	1.669
r_angle_other_deg	1.336
r_nbd_other	0.237
r_nbd_refined	0.22
r_symmetry_nbd_other	0.206
r_symmetry_xyhbond_nbd_refined	0.161
r_nbtor_refined	0.158
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1820
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing