1S5B | pdb_00001s5b

Cholera holotoxin with an A-subunit Y30S mutation Form 3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LTG	PDB ENTRIES 1LTG, 3CHB
experimental model	PDB	3CHB	PDB ENTRIES 1LTG, 3CHB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PEG 2000mme, MES, kemptide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.104	α = 90
b = 107.431	β = 91.29
c = 65.95	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	ADSC QUANTUM 210		2002-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9800	ALS	5.0.2

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	2.13	20.02	99.6	0.096	12.1	3.2	46304	46304

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	2.13	2.21	99.8		0.392	3.3		4648

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 ENTRIES 1LTG, 3CHB	2.13	20.02	43956	43956	2340	99.29	0.17988	0.17988	0.1775	0.19	0.22425	0.23	RANDOM	12.395

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]
-0.11		-0.06	0.13		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.546
r_mcangle_it	1.436
r_scangle_it	1.432
r_angle_refined_deg	1.282
r_scbond_it	0.91
r_mcbond_it	0.887
r_angle_other_deg	0.704
r_symmetry_vdw_other	0.303
r_symmetry_hbond_refined	0.273
r_nbd_other	0.263
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.205
r_symmetry_vdw_refined	0.194
r_metal_ion_refined	0.133
r_nbtor_other	0.09
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5647
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing