3ONP

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	297	0.17 M Ammonium Acetate, 0.085 M Na Citrate pH 5.6, 25.5% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.782	α = 90
b = 74.782	β = 90
c = 139.105	γ = 120

Symmetry
Space Group	P 65 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 QUANTUM 315r	mirrors	2010-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	50	99.9	0.08	12.7	17.2	18791	18791			36.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.93	99.6		0.786	2.58	10.2	904

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	50	17764	17764	961	99.34	0.191	0.191	0.189	0.219	RANDOM	40.863

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]
-0.43	-0.22		-0.43		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.402
r_dihedral_angle_4_deg	20.397
r_dihedral_angle_3_deg	18.109
r_dihedral_angle_1_deg	5.663
r_scangle_it	5.252
r_scbond_it	3.06
r_mcangle_it	2.219
r_angle_refined_deg	1.505
r_mcbond_it	1.209
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1218
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing