3CGG | pdb_00003cgg

Crystal structure of TehB-like SAM-dependent methyltransferase (NP_600671.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	277	NANODROP, 1.0M Sodium citrate, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.33	α = 90
b = 87.398	β = 90
c = 92.429	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-01-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97978	SSRL	BL9-2

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	2	29.062	99.9	0.093	0.093	6.6	3.6		28773			28.45

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	2	2.05	100		0.667	0.667	1.1	3.7	2095

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	29.062	28741	1455	99.74	0.169	0.167	0.17	0.212	0.22	RANDOM	25.751

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]
-0.23			0.58		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.979
r_dihedral_angle_4_deg	21.126
r_dihedral_angle_3_deg	15.032
r_scangle_it	6.516
r_dihedral_angle_1_deg	6.071
r_scbond_it	4.842
r_mcangle_it	2.793
r_mcbond_it	1.872
r_angle_refined_deg	1.827
r_angle_other_deg	0.987
r_mcbond_other	0.598
r_symmetry_vdw_other	0.23
r_symmetry_vdw_refined	0.203
r_nbd_other	0.202
r_nbd_refined	0.199
r_nbtor_refined	0.174
r_chiral_restr	0.167
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.117
r_nbtor_other	0.087
r_xyhbond_nbd_other	0.073
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2820
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
autoSHARP	phasing
SHELXD	phasing