3C4Q | pdb_00003c4q

Structure of the retaining glycosyltransferase MshA : The first step in mycothiol biosynthesis. Organism : Corynebacterium glutamicum- Complex with UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C48	PDB entry 3C48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	298	Protein (40 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME, 10 mM UDPNAG) Precipitant (0.8 M sodium citrate pH 5.5 ), Vapor diffusion under oil, temperature 298K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 224.245	α = 90
b = 224.245	β = 90
c = 125.112	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315	Meridionally-bent fused silica mirror with palladium and uncoated stripes	2007-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9778	NSLS	X25

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	2.8	80	96	0.066	0.066	22.4	5.4	37594	37594			69.2

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	2.8	2.95	96.8		0.318	0.318	3.9	5.3	5474

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3C48	2.8	78.25	35709	35709	1885	95.47	0.18547	0.18547	0.18379	0.18	0.21754	0.22	RANDOM	28.568

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]
-0.85			-0.85		1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.529
r_dihedral_angle_4_deg	23.204
r_dihedral_angle_3_deg	19.463
r_dihedral_angle_1_deg	8.363
r_scangle_it	2.943
r_scbond_it	1.736
r_angle_refined_deg	1.733
r_mcangle_it	1.107
r_mcbond_it	0.62
r_symmetry_hbond_refined	0.329
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.235
r_chiral_restr	0.169
r_xyhbond_nbd_refined	0.134
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6051
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing