3KR9

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop		298	2.0M ammonium sulfate, 0.1M tri-sodium citrate pH5.6, 0.2M sodium/potassium tartrate, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	58.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.807	α = 90
b = 58.668	β = 90
c = 142.995	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD				M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.97888, 0.97917, 0.96395	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	71.43					20787

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	2	71.43	20787	1064	98.23	0.236	0.234	0.289	RANDOM	28.211

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]
-1.78			-1.32		3.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.732
r_dihedral_angle_3_deg	16.68
r_dihedral_angle_4_deg	15.611
r_dihedral_angle_1_deg	6.075
r_scangle_it	4.809
r_scbond_it	3.081
r_angle_refined_deg	1.695
r_mcangle_it	1.67
r_mcbond_it	0.973
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.732
r_dihedral_angle_3_deg	16.68
r_dihedral_angle_4_deg	15.611
r_dihedral_angle_1_deg	6.075
r_scangle_it	4.809
r_scbond_it	3.081
r_angle_refined_deg	1.695
r_mcangle_it	1.67
r_mcbond_it	0.973
r_chiral_restr	0.13
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1735
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.