1SGK

NUCLEOTIDE-FREE DIPHTHERIA TOXIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DDT	DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		HANGING DROP, 12 % PEG8000, 0.43M NACL, 0.043M TRIS, PH 7.5, vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.67	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.2	α = 90
b = 91.2	β = 94.2
c = 65.3	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	94	IMAGE PLATE	RIGAKU		1994-04-15	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

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	2.2		95.7	0.066	9.6	2.8		26627			33.9

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	2.3	2.4	92.7		0.239	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-FACTOR	DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT)	2.3	8	25726	2565	96.2	0.182	0.182	0.282	RANDOM	38.8

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	24.3
x_angle_deg	1.5
x_improper_angle_d	1.4
x_bond_d	0.01
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4021
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms

Software

Software
Software Name	Purpose
R-AXIS	data collection
R-AXIS	data reduction
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data scaling
X-PLOR	phasing