3C48 | pdb_00003c48

Structure of the retaining glycosyltransferase MshA: The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum- APO (OPEN) structure.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	Protein (15 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME): Precipitant (20% Peg4000, 100 mM Tris pH 8.5, 200 mm LiSO4), Vapor diffusion under oil, temperature 291K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.743	α = 90
b = 79.743	β = 90
c = 148.364	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2007-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.1	35	98.7	0.052	0.052	16.5	2.9	178087	60789			35.7

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	2.1	2.21	91.5		0.238	0.238	2.9	2.5	8239

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2.1	34.53	57704	57704	3079	98.67	0.18222	0.18222	0.18014	0.18	0.22173	0.22	RANDOM	36.496

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]
-0.19	-0.1		-0.19		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.319
r_dihedral_angle_4_deg	15.793
r_dihedral_angle_3_deg	14.643
r_dihedral_angle_1_deg	7.163
r_scangle_it	3.139
r_scbond_it	2.084
r_angle_refined_deg	1.521
r_mcangle_it	1.28
r_mcbond_it	0.805
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.319
r_dihedral_angle_4_deg	15.793
r_dihedral_angle_3_deg	14.643
r_dihedral_angle_1_deg	7.163
r_scangle_it	3.139
r_scbond_it	2.084
r_angle_refined_deg	1.521
r_mcangle_it	1.28
r_mcbond_it	0.805
r_nbtor_refined	0.297
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6148
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

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.