3O4V

Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	298	60 mM Sodium acetate, pH 4.6, 35% (v/v) isopropanol, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 69.09	β = 90
c = 128.31	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2005-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.542

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	1.75	32.93	98.8	0.049	29.5	12.31		46533

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)
	1.75	1.81	95.1		0.284	7.8	10.3	4408

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.75	21.39	46449	4679	98.59	0.1565	0.1523	0.1945	RANDOM	14.5508

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]
0.06			-0.09		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.769
r_dihedral_angle_4_deg	21.841
r_dihedral_angle_3_deg	11.714
r_dihedral_angle_1_deg	6.274
r_scangle_it	5.383
r_scbond_it	3.286
r_angle_refined_deg	2.063
r_mcangle_it	2
r_mcbond_it	1.241
r_chiral_restr	0.203

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.769
r_dihedral_angle_4_deg	21.841
r_dihedral_angle_3_deg	11.714
r_dihedral_angle_1_deg	6.274
r_scangle_it	5.383
r_scbond_it	3.286
r_angle_refined_deg	2.063
r_mcangle_it	2
r_mcbond_it	1.241
r_chiral_restr	0.203
r_bond_refined_d	0.03
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3435
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	80

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.