5DAZ

Crystal structure of Scabin, a mono-ADP-ribosyltransferase from Streptomyces scabies

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	100 mM MES, pH 6.5, 15% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.787	α = 90
b = 61.075	β = 99.64
c = 37.812	γ = 90

Symmetry
Space Group	C 1 2 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 MX-300		2014-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.979	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.45	43.273	94.4	0.042	0.048	18.81			33118		-3	26.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.54	81		0.764	0.876	2.15

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	PDB entry 2CB4	1.45	43.27	31437	1655	94.75	0.1668	0.1649	0.2021	RANDOM	27.961

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]
-0.18		0.5	0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.384
r_dihedral_angle_4_deg	19.897
r_dihedral_angle_3_deg	13.359
r_dihedral_angle_1_deg	8.317
r_mcangle_it	3.538
r_angle_refined_deg	2.81
r_mcbond_it	2.346
r_mcbond_other	2.335
r_angle_other_deg	1.366
r_chiral_restr	0.166

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.384
r_dihedral_angle_4_deg	19.897
r_dihedral_angle_3_deg	13.359
r_dihedral_angle_1_deg	8.317
r_mcangle_it	3.538
r_angle_refined_deg	2.81
r_mcbond_it	2.346
r_mcbond_other	2.335
r_angle_other_deg	1.366
r_chiral_restr	0.166
r_bond_refined_d	0.033
r_gen_planes_refined	0.017
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1313
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

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.