1PZI | pdb_00001pzi

Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Galactoside 2a

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	32% PEG 5000, 100 mM Tris-HCl pH 7.8, 50 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.96	36.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.817	α = 90
b = 78.683	β = 116.2
c = 62.3	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	SBC-2		2002-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.99	50	95.3	0.061	19.28	3.45	34499	34499			20.322

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.99	2.07	84.1		0.145	7.07	2.27	3005

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1DJR	1.99	27.95	34499	32749	1731	95.21	0.15778	0.15778	0.15449	0.17	0.2207	0.23	RANDOM	15.815

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]
0.01		0.03	0.03		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.338
r_scangle_it	4.461
r_scbond_it	3.017
r_mcangle_it	2.433
r_mcbond_it	1.656
r_angle_refined_deg	1.158
r_angle_other_deg	0.651
r_symmetry_vdw_other	0.304
r_symmetry_vdw_refined	0.297
r_nbd_other	0.29
r_symmetry_hbond_refined	0.244
r_xyhbond_nbd_refined	0.219
r_nbd_refined	0.21
r_nbtor_other	0.088
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4120
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	168

Software

Software
Software Name	Purpose
REFMAC	refinement
TRUNCATE	data reduction
XTALVIEW	refinement
HKL-2000	data collection
HKL-2000	data reduction
CCP4	data scaling