1RF2 | pdb_00001rf2

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4

X-RAY DIFFRACTION

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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	16% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.235	α = 90
b = 66.028	β = 105.8
c = 78.642	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		2003-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9626	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	94.2	0.081	13.5	3.5	111363	104314		-3	13.4

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	69.3		0.591	1.8	2.7	7606

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	PDB ENTRY 3CHB	1.35	49.39	104314	104314	5219	93.89	0.13439	0.13439	0.13232	0.16	0.17389	0.19	RANDOM	10.455

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]
0.04		0.03	-0.06		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	21.151
r_scangle_it	7.194
r_dihedral_angle_1_deg	6.954
r_sphericity_bonded	6.669
r_scbond_it	5.237
r_mcangle_it	3.398
r_mcbond_it	2.485
r_rigid_bond_restr	2.121
r_angle_refined_deg	1.417
r_angle_other_deg	0.862
r_symmetry_vdw_other	0.348
r_nbd_other	0.298
r_symmetry_hbond_refined	0.265
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.086
r_nbtor_other	0.086
r_bond_refined_d	0.012
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	4074
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	138

Software

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