3KU1

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase, in complex with S-adenosyl-L-methionine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	1.6M tri-sodium citrate (pH5.6), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.752	α = 90
b = 142.752	β = 90
c = 148.163	γ = 120

Symmetry
Space Group	P 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 210		2008-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	3	50		0.087	0.087	22.8	5.7		67466

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3KR9	3	47.46	64055	3411	99.79	0.246	0.244	0.296	RANDOM	83.49

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]
0.28	0.14		0.28		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.657
r_dihedral_angle_3_deg	23.075
r_dihedral_angle_4_deg	20.96
r_dihedral_angle_1_deg	8.108
r_scangle_it	3.805
r_scbond_it	2.213
r_angle_refined_deg	2.081
r_mcangle_it	1.495
r_mcbond_it	0.858
r_symmetry_vdw_refined	0.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.657
r_dihedral_angle_3_deg	23.075
r_dihedral_angle_4_deg	20.96
r_dihedral_angle_1_deg	8.108
r_scangle_it	3.805
r_scbond_it	2.213
r_angle_refined_deg	2.081
r_mcangle_it	1.495
r_mcbond_it	0.858
r_symmetry_vdw_refined	0.445
r_nbtor_refined	0.326
r_symmetry_hbond_refined	0.299
r_nbd_refined	0.28
r_xyhbond_nbd_refined	0.21
r_chiral_restr	0.13
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13374
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	108

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.