3HZS | pdb_00003hzs

S. aureus monofunctional glycosyltransferase (MtgA)in complex with moenomycin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Unpublished apo structure of MTGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	Sa MtgA E100Q at 10 mg/ml was mixed with 1mM Moenomycin and 1mM MnCl2 and incubated on ice for ~3 hours. Precipitated material was removed by centrifugation at 16,000xg for 5 minutes. The Mmoenomycin complex was crystallized by hanging drop vapor diffusion, mixing the protein 1:1 with a reservoir solution containing 0.1M Na Acetate pH 4.6, 0.2M NaCl, 30% MPD at 22oC. Hexagonal plate crystals formed in 1 week., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.422	α = 90
b = 114.422	β = 90
c = 128.844	γ = 120

Symmetry
Space Group	H 3 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	RIGAKU SATURN 944	Rigaku Varimax HF optics	2007-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	23.12	99.9	0.173	13.6	3.9		45531	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.2	100		0.381	3.2	3.8	4606

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	Unpublished apo structure of MTGA	2.1	23.12	2	2	45531	18121	963	99.69	0.19183	0.18917	0.1921	0.24379	0.249	RANDOM	36.033

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]
-2.03	-1.02		-2.03		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.965
r_dihedral_angle_4_deg	21.85
r_dihedral_angle_3_deg	14.695
r_scangle_it	7.279
r_dihedral_angle_1_deg	5.865
r_scbond_it	5.623
r_mcangle_it	3.675
r_mcbond_it	2.401
r_angle_refined_deg	1.8
r_chiral_restr	0.169
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1708
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	105

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling