3FUU | pdb_00003fuu

T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with Adenosine in space group P212121

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch technique under oil	7.5	277	50 mM magnesium chloride hexahydrate, 100 mM HEPES (pH 7.5) and 30% v/v polyethylene glycol monomethyl ether 550, microbatch technique under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.195	α = 90
b = 61.263	β = 90
c = 82.719	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	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	1.53	25	98.3	0.077	18.27	4.3		41095

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	1.53	1.57	99.6		0.41	2.2	4.2	4080

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.53	25	40638	2054	97.96	0.215	0.213	0.21	0.258	0.25	RANDOM	25.428

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]
0.66			-0.25		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.768
r_dihedral_angle_4_deg	15.995
r_dihedral_angle_3_deg	12.529
r_dihedral_angle_1_deg	5.992
r_scangle_it	2.907
r_scbond_it	1.935
r_angle_refined_deg	1.414
r_mcangle_it	1.075
r_mcbond_it	0.723
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.768
r_dihedral_angle_4_deg	15.995
r_dihedral_angle_3_deg	12.529
r_dihedral_angle_1_deg	5.992
r_scangle_it	2.907
r_scbond_it	1.935
r_angle_refined_deg	1.414
r_mcangle_it	1.075
r_mcbond_it	0.723
r_nbtor_refined	0.309
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2061
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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 R01GM157729.