3AI9

Crystal structure of DUF358 protein reveals a putative SPOUT-class rRNA methyltransferase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG, Mg, Tris, Ammonium Fluoride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.288	α = 90
b = 48.133	β = 126.09
c = 62.362	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			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9797, 0.9799, 0.95	NSLS	X12C

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	1.55	50	85.4	0.038	36.1	3.4		25283

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)
	1.55	1.61	56.2		0.321	2.5	2.8

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	MAD	THROUGHOUT	1.55	34.06	25283	1356	90.49	0.19193	0.18952	0.23682	RANDOM	33.53

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]
3.49		-0.37	-1.17		-2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.498
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	14.689
r_dihedral_angle_1_deg	6.123
r_scangle_it	4.225
r_scbond_it	2.829
r_mcangle_it	1.647
r_angle_refined_deg	1.644
r_mcbond_it	1.169
r_symmetry_vdw_refined	0.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.498
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	14.689
r_dihedral_angle_1_deg	6.123
r_scangle_it	4.225
r_scbond_it	2.829
r_mcangle_it	1.647
r_angle_refined_deg	1.644
r_mcbond_it	1.169
r_symmetry_vdw_refined	0.346
r_nbtor_refined	0.315
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.106
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1706
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	22

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.