1VKY | pdb_00001vky

Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		295	0.10M NP_Citrate 1, 4.0% NP_Peg 6000, % NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	0.10M NP_Citrate 2, 12.0% NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.78
3.66	66.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.033	α = 90
b = 122.843	β = 90
c = 131.207	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		2003-10-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	APS		2003-08-06	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934,1.00800,0.97921	APS	19-ID

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	2	29.39	100	0.073	14.8	7.3		65036			44.87

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	2	2.11	100		0.678	2.7	6.4	9393

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	29.39	61756	3280	99.94	0.18107	0.17951	0.19	0.21041	0.22	RANDOM	32.15

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]
-2.08			1.47		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.747
r_dihedral_angle_4_deg	15.993
r_dihedral_angle_3_deg	14.577
r_scangle_it	7.898
r_dihedral_angle_1_deg	6.183
r_scbond_it	5.39
r_mcangle_it	3.29
r_mcbond_it	2.294
r_angle_refined_deg	1.529
r_angle_other_deg	0.805
r_mcbond_other	0.652
r_symmetry_vdw_other	0.287
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.192
r_nbd_other	0.19
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.092
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4501
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing