3FZY | pdb_00003fzy

Crystal Structure of Pre-cleavage Form of Cysteine Protease Domain from Vibrio cholerae RtxA Toxin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EEB	PDB entry 3EEB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	The PEGs II Suite, condition 72 mixed 1:1 v/v with 7.3mg/mL protein, 0.3M NaCl, 0.5mM InsP6, 10mM Tris-HCl (pH 7.4), VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.055	α = 90
b = 66.373	β = 90
c = 137.958	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	MARMOSAIC 225 mm CCD	beryllium lenses	2008-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.95	25	99.4	0.076		6.7	32396	32396		-3	33.5

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	1.95	1.98	95.3		0.448	3.1	3.9	1524

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 3EEB	1.95	23.67	29932	29932	1584	99.62	0.1713	0.1713	0.16893	0.24	0.21616	0.27	RANDOM	32.053

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]
2.94			-3.42		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.739
r_dihedral_angle_4_deg	13.979
r_dihedral_angle_3_deg	11.971
r_scangle_it	4.773
r_dihedral_angle_1_deg	4.556
r_scbond_it	3.237
r_mcangle_it	2.062
r_angle_refined_deg	1.696
r_mcbond_it	1.259
r_angle_other_deg	0.966

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.739
r_dihedral_angle_4_deg	13.979
r_dihedral_angle_3_deg	11.971
r_scangle_it	4.773
r_dihedral_angle_1_deg	4.556
r_scbond_it	3.237
r_mcangle_it	2.062
r_angle_refined_deg	1.696
r_mcbond_it	1.259
r_angle_other_deg	0.966
r_mcbond_other	0.407
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3274
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	85

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.