3C8Z | pdb_00003c8z

The 1.6 A Crystal Structure of MshC: The Rate Limiting Enzyme in the Mycothiol Biosynthetic Pathway

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		de novo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	under oil	7.9	291	0.1 M HEPES pH 7.9, 2 M NH4SO4, 2% PEG400, under oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.521	α = 90
b = 123.521	β = 90
c = 186.026	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9486, 1.1	NSLS	X12C

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	1.6	37.09	99.8	0.062	0.057	37	4		131763

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)
	1.6	1.64	98.3		0.349	0.403	3.1	3.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD and Molecular Replacement	THROUGHOUT	de novo	1.6	37.09	138721	131736	6973	99.74	0.18594	0.18485	0.18	0.20668	0.21	RANDOM	24.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.902
r_dihedral_angle_4_deg	17.821
r_dihedral_angle_3_deg	12.92
r_dihedral_angle_1_deg	11.396
r_scangle_it	3.215
r_scbond_it	2.072
r_angle_refined_deg	1.656
r_mcangle_it	1.344
r_mcbond_it	0.825
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.902
r_dihedral_angle_4_deg	17.821
r_dihedral_angle_3_deg	12.92
r_dihedral_angle_1_deg	11.396
r_scangle_it	3.215
r_scbond_it	2.072
r_angle_refined_deg	1.656
r_mcangle_it	1.344
r_mcbond_it	0.825
r_nbtor_refined	0.303
r_chiral_restr	0.298
r_symmetry_hbond_refined	0.207
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.162
r_xyhbond_nbd_refined	0.116
r_metal_ion_refined	0.021
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6218
Nucleic Acid Atoms
Solvent Atoms	868
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building

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.