3NDI | pdb_00003ndi

X-ray Structure of a C-3'-Methyltransferase in Complex with S-adenosylmethionine and dTMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In-house MIR model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.3 M - 1.5 M Sodium/potassium Phosphate, 10 mM Deoxythymidine 5'-monophosphate, 5 mM S-adenosyl methionine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.963	α = 90
b = 114.385	β = 90
c = 37.782	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	Bruker Platinum 135	Montel	2010-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54178

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	1.5	50.5	96	0.084	0.084	10.71	4.51	71338	68520

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.59	88.8		0.35	0.35	2.65	2.53	10144

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	In-house MIR model	1.5	50	68409	64961	3448	96.2	0.197	0.19655	0.19468	0.1905	0.23188	0.2239	RANDOM	12.091

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]
-0.22			-0.32		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.495
r_dihedral_angle_4_deg	17.402
r_dihedral_angle_3_deg	13.324
r_dihedral_angle_1_deg	6.286
r_scangle_it	5.87
r_scbond_it	3.97
r_mcangle_it	2.604
r_angle_refined_deg	2.126
r_mcbond_it	1.767
r_chiral_restr	0.148
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3162
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	59

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling