3FUT

Apo-form of T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in space group P21212

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch technique under oil		277	200 mM di-ammonium hydrogen phosphate and 20% w/v polyethylene glycole 3350, microbatch technique under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.046	α = 90
b = 53.692	β = 90
c = 69.354	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 130 mm	Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror			SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9797	NSLS	X4C

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	1.52	50	94.5	0.039	34.67	5		77536

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	1.52	1.56	71.8		0.25	4.27	3.5	11180

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		THROUGHOUT	1.52	25.04	77536	3868	97.46	0.206	0.204	0.241	RANDOM	17.129

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.764
r_dihedral_angle_4_deg	14.12
r_dihedral_angle_3_deg	13.961
r_dihedral_angle_1_deg	5.296
r_scangle_it	2.96
r_scbond_it	1.901
r_angle_refined_deg	1.334
r_mcangle_it	1.12
r_mcbond_it	0.774
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.764
r_dihedral_angle_4_deg	14.12
r_dihedral_angle_3_deg	13.961
r_dihedral_angle_1_deg	5.296
r_scangle_it	2.96
r_scbond_it	1.901
r_angle_refined_deg	1.334
r_mcangle_it	1.12
r_mcbond_it	0.774
r_nbtor_refined	0.308
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.185
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4094
Nucleic Acid Atoms
Solvent Atoms	768
Heterogen Atoms

Software

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

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.