4KGN

Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	BupsA.00072.a.A1 PW25076 at 25 mg/mL with 3 mM SAH against Morpheus screen condition G12, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02 M each carboxylate: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate, 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 236960g12, unique puck ID qoj5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 149.71	β = 90.49
c = 80.3	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-300		2013-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.15	50	98.1	0.073	13.84	3.9	67356	66051		-3

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	2.15	2.21	97.4		0.461	2.92

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.15	44.17	62704	3346	95.73	0.17043	0.1692	0.19333	RANDOM	31.742

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]
11.72		-7.22	-0.09		-11.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.41
r_dihedral_angle_4_deg	16.358
r_dihedral_angle_3_deg	13.379
r_dihedral_angle_1_deg	5.851
r_mcangle_it	1.994
r_angle_refined_deg	1.42
r_scbond_it	1.303
r_mcbond_it	1.194
r_mcbond_other	1.194
r_angle_other_deg	0.789
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9167
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	110

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction