3G2O | pdb_00003g2o

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G2M	PDB ENTRY 3G2M

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
2.58	52.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.917	α = 90
b = 72.335	β = 103.89
c = 75.306	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	MAR CCD 165 mm		2007-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9798	APS	31-ID

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	2.1	50	90.8	0.04	26.008	3.5		35055			38.3

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	2.1	2.18	60.9		0.276		2.6	2346

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3G2M	2.1	42.37	35029	1783	90.58	0.218	0.216	0.21	0.245	0.24	RANDOM	48.143

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]
-1.31		-0.49	1.99		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.437
r_dihedral_angle_4_deg	19.041
r_dihedral_angle_3_deg	15.5
r_dihedral_angle_1_deg	6.16
r_scangle_it	3.026
r_scbond_it	1.855
r_mcangle_it	1.424
r_angle_refined_deg	1.3
r_mcbond_it	0.889
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.437
r_dihedral_angle_4_deg	19.041
r_dihedral_angle_3_deg	15.5
r_dihedral_angle_1_deg	6.16
r_scangle_it	3.026
r_scbond_it	1.855
r_mcangle_it	1.424
r_angle_refined_deg	1.3
r_mcbond_it	0.889
r_nbtor_refined	0.298
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3603
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	54

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
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 R01GM157729.