3G2P

Crystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with (S)-adenosyl-L-homocysteine (SAH)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	0.1M MES pH 6.5, 18% PEG-monomethyl ether 5K, vapor diffusion, hanging drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.469	α = 90
b = 72.451	β = 104.19
c = 75.246	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	IMAGE PLATE	RIGAKU RAXIS HTC		2007-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.95	50	97.5	0.112	12.124	3.7		13628			76.2

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	2.95	3.07	96.3		0.5		3.7	1342

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 3G2M	2.95	50	13628	684	96.96	0.211	0.209	0.259	RANDOM	50.76

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]
-2.82		-0.22	3.65		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.165
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	18.691
r_dihedral_angle_1_deg	6.728
r_scangle_it	2.226
r_angle_refined_deg	1.49
r_scbond_it	1.304
r_mcangle_it	1.089
r_mcbond_it	0.628
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.165
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	18.691
r_dihedral_angle_1_deg	6.728
r_scangle_it	2.226
r_angle_refined_deg	1.49
r_scbond_it	1.304
r_mcangle_it	1.089
r_mcbond_it	0.628
r_nbtor_refined	0.311
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.093
r_symmetry_hbond_refined	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3703
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	45

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM133198.