3NY6 | pdb_00003ny6

Catalytic fragment of cholix toxin from vibrio cholerae in complex with inhibitor V30

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q6M	PDB entry 2Q6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	15% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.489	α = 90
b = 64.973	β = 90
c = 86.603	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm	Multilayer mirror, curved to focus in the vertical (R = 400 m)	2010-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.03796	MAX II	I911-2

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	1.68	30	99.8	0.058	19.59	5.6	23603	23558		-3	23.237

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)
	1.68	1.72	99.9		0.523	3.7	5.4	1695

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 (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 2Q6M	1.68	29.31	23557	23557	1178	100	0.176	0.174	0.19	0.2	0.22	RANDOM	17.342

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
r_dihedral_angle_2_deg	31.332
r_dihedral_angle_4_deg	16.869
r_dihedral_angle_3_deg	13.44
r_dihedral_angle_1_deg	5.797
r_scangle_it	3.032
r_scbond_it	1.869
r_angle_refined_deg	1.363
r_mcangle_it	1.061
r_mcbond_it	0.622
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.332
r_dihedral_angle_4_deg	16.869
r_dihedral_angle_3_deg	13.44
r_dihedral_angle_1_deg	5.797
r_scangle_it	3.032
r_scbond_it	1.869
r_angle_refined_deg	1.363
r_mcangle_it	1.061
r_mcbond_it	0.622
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1547
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

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.