1RDP

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CHB	PDB ENTRY 3CHB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	12% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.09	α = 90
b = 66.079	β = 105.83
c = 78.715	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	ADSC QUANTUM 315		2003-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9791	ALS	8.2.2

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	1.35	50	91.3	0.059	19.5	3.66	105335	100384		-3	12.9

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)
	1.35	1.4	63.8		0.451	2.4	3.22	6952

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CHB	1.35	48.22	100384	100384	5029	91.22	0.13194	0.13194	0.12986	0.17052	RANDOM	10.928

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		-0.03	0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	21.699
r_dihedral_angle_1_deg	6.952
r_scangle_it	6.083
r_sphericity_bonded	6.002
r_scbond_it	4.376
r_mcangle_it	3.476
r_mcbond_it	2.658
r_rigid_bond_restr	2.112
r_angle_refined_deg	1.501
r_angle_other_deg	0.867
r_symmetry_vdw_other	0.355
r_nbd_other	0.297
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.088
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4093
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	140

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
XTALVIEW	refinement