1HQ0 | pdb_00001hq0

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E.COLI CYTOTOXIC NECROTIZING FACTOR TYPE 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	310	Sodium phosphate, potassium phosphate, 1,4-butanediol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Properties
Matthews coefficient	Solvent content
2.358	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55	α = 90
b = 55	β = 90
c = 176.2	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	focusing mirrors	2000-03-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2000-04-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54180
2	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.97943, 0.980035, 0.925256, 1.06883	SSRL	BL1-5

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	1.76	20	99.9	0.056	36.7	8.7	29261	26431		-3	20.7

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)
	1.76	1.81	99.5		0.757	2.6	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.83	20	26457	26447	1306	100	0.193	0.193	0.191	0.19	0.214	0.22	Random 5% of data	28.05

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]
2.93	1.98		2.93		-5.85

RMS Deviations
Key	Refinement Restraint Deviation
x_torsion_deg	25.9
x_scangle_it	4.78
x_scbond_it	3.74
x_mcangle_it	3.48
x_mcbond_it	2.48
x_angle_deg	1.2
x_torsion_impr_deg	0.69
x_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2262
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	15

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.