3HIW

Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	20% PEG2000MME, 0.1M sodium acetate, 0.4M potassium thiocyanate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.555	α = 78.87
b = 52.573	β = 66.32
c = 54.369	γ = 80.58

Symmetry
Space Group	P 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	ADSC QUANTUM 315		2008-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	1.8	20	97.1	0.041	18.983	1.9		44853

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)
	1.8	1.86	95.6		0.216		1.9	4409

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	1.8	19.64	44846	2276	96.91	0.184	0.181	0.223	RANDOM	17.906

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]
0.07	0.02	-0.05	-0.07	0.06	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.204
r_dihedral_angle_4_deg	18.415
r_dihedral_angle_3_deg	13.131
r_dihedral_angle_1_deg	5.216
r_scangle_it	3.081
r_scbond_it	1.806
r_angle_refined_deg	1.325
r_mcangle_it	1.117
r_mcbond_it	0.619
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.204
r_dihedral_angle_4_deg	18.415
r_dihedral_angle_3_deg	13.131
r_dihedral_angle_1_deg	5.216
r_scangle_it	3.081
r_scbond_it	1.806
r_angle_refined_deg	1.325
r_mcangle_it	1.117
r_mcbond_it	0.619
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4030
Nucleic Acid Atoms
Solvent Atoms	442
Heterogen Atoms	212

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	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.