4E2X | pdb_00004e2x

X-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and dTDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NDJ	PDB ENTRY 3NDJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.2-1.6 M sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.542	α = 90
b = 114.174	β = 90
c = 37.632	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	2011-05-12	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	1.4	38	94.7	0.072	0.072	10.3	4.3	86374	81798

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	1.4	1.5	85.2		0.34	0.34	1.83	1.74	13540

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NDJ	1.4	38	81756	77644	4112	94.74	0.20607	0.20447	0.23641	0.1992	RANDOM	14.959

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]
-0.36			0.19		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.554
r_dihedral_angle_4_deg	20.144
r_dihedral_angle_3_deg	13.295
r_scangle_it	6.875
r_dihedral_angle_1_deg	6.652
r_scbond_it	4.375
r_mcangle_it	2.853
r_angle_refined_deg	2.267
r_mcbond_it	1.962
r_chiral_restr	0.168
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3161
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	68

Software

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