2ASH

Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		10	293	15.0% PEG-8000, 0.2M NaCl, 0.1M CHES pH 10.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.467	α = 90
b = 99.422	β = 123.8
c = 124.163	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 210		2004-03-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210	KOHZU: double crystal Si(111)	2004-02-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000	ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115902, 1.282804	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	51.7	99.4	0.059	0.059	6.6	3.4		133817

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	1.95		99.8	0.659	0.659	0.4	2.9

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD, MOLECULAR REPLACEMENT	THROUGHOUT	1EFZ	1.9	51.7	124830	6626	96.9	0.195	0.193	0.229	RANDOM	22.259

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]
-0.89		-0.04	0.49		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.766
r_dihedral_angle_4_deg	16.007
r_dihedral_angle_3_deg	13.827
r_dihedral_angle_1_deg	6.195
r_scangle_it	3.696
r_scbond_it	2.458
r_angle_refined_deg	1.583
r_mcangle_it	1.475
r_angle_other_deg	1.009
r_mcbond_it	0.989
r_symmetry_vdw_other	0.329
r_symmetry_vdw_refined	0.297
r_symmetry_hbond_refined	0.242
r_mcbond_other	0.238
r_nbd_refined	0.208
r_nbd_other	0.199
r_nbtor_refined	0.183
r_metal_ion_refined	0.161
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.094
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11070
Nucleic Acid Atoms
Solvent Atoms	655
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing
MOLREP	phasing