3DCM | pdb_00003dcm

Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	297	100mM Tris-HCl pH 7.0, 200mM calcium acetate, 20% (v/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.648	α = 90
b = 63.402	β = 129.03
c = 54.522	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	Bruker Platinum 135		2004-10-21	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	Bruker Platinum 135		2004-10-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6B	1.0000	PAL/PLS	6B
2	SYNCHROTRON	PAL/PLS BEAMLINE 6B	1.07163, 1.07204, 1.06261	PAL/PLS	6B

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
1,2	2	20	98.4	0.071	14.5	4.6		14038

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)
	2	2.07	91.2		0.247		4.1	1282

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	MAD	THROUGHOUT	2	17.43	14038	1412	98.17	0.201	0.198	0.1966	0.235	0.2314	RANDOM	24.379

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]
0.89		-0.51	-1.94		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.469
r_dihedral_angle_3_deg	15.828
r_dihedral_angle_4_deg	14.518
r_dihedral_angle_1_deg	10.967
r_scangle_it	2.614
r_scbond_it	1.608
r_angle_refined_deg	1.417
r_mcangle_it	1.107
r_mcbond_it	0.858
r_chiral_restr	0.361
r_nbtor_refined	0.3
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.137
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1515
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	27

Software

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