4X24

Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	295	Protein (10 mg/mL); Reservoir (0.2M ammonium chloride pH 6.3 and 20% PEG 3350); Cryoprotection (20% (v/v) glycerol)

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.898	α = 90
b = 72.708	β = 110
c = 61.621	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX225HE		2014-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	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	1.5	50	99.1	0.082	8.9	3.6		69602			13.2

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	1.5	1.53	96.8		0.685	1.78	3.5	3351

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DP9	1.5	30	66097	3448	99.09	0.1696	0.1687	0.1866	RANDOM	17.318

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		-0.24	-0.12		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.259
r_dihedral_angle_4_deg	13.133
r_dihedral_angle_3_deg	11.333
r_dihedral_angle_1_deg	5.866
r_angle_refined_deg	1.455
r_mcangle_it	1.403
r_angle_other_deg	0.972
r_mcbond_it	0.874
r_mcbond_other	0.874
r_chiral_restr	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.259
r_dihedral_angle_4_deg	13.133
r_dihedral_angle_3_deg	11.333
r_dihedral_angle_1_deg	5.866
r_angle_refined_deg	1.455
r_mcangle_it	1.403
r_angle_other_deg	0.972
r_mcbond_it	0.874
r_mcbond_other	0.874
r_chiral_restr	0.154
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3509
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	50

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.