1QNU | pdb_00001qnu

Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BOS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (28% SA NH4SO4, 2% 2-METHYL-2,4-PENTANEDIOL, 0.1M NACL, 0.1 M HEPES, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.39	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.47	α = 90
b = 71.61	β = 109.02
c = 56.36	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	287	IMAGE PLATE	MARRESEARCH	YALE MIRRORS	1999-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU/MSC RU-

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	2.23	50	99	0.148	0.148	3.4	5.3		19159			12.8

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	2.23	2.35	96.2		0.291	0.291	2.1	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BOS	2.23	50	19150	1064	99.2	0.171	0.171	0.17	0.184	0.18	SHELLS	26.3

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]
1.2		2.85	5		-6.19

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25
c_scangle_it	3.18
c_scbond_it	2.05
c_mcangle_it	1.66
c_angle_deg	1.3
c_mcbond_it	1.08
c_improper_angle_d	0.7
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2700
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	240

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing