3C1Q | pdb_00003c1q

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VMA	2vma, 2vmb
experimental model	PDB	2VMB	2vma, 2vmb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1ul protein at 10mg/ml + 1ul reservoir: 12.5% PEG 400, 200mM CaOAc2, 100mM MES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.988	α = 90
b = 52.122	β = 90
c = 89.47	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	RIGAKU SATURN 944	multilayer (Varimax)	2006-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	45.05	95.6	0.06	0.06	15	3.78	23838	23838			17.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	79.1		0.223	0.223	3.3	1.97	1347

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	2vma, 2vmb	1.7	33.94	22632	22632	1223	95.96	0.15846	0.15846	0.15587	0.17	0.20793	0.21	RANDOM	9.193

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]
			0.48		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.167
r_dihedral_angle_4_deg	15.622
r_dihedral_angle_3_deg	10.964
r_dihedral_angle_1_deg	3.925
r_scangle_it	3.178
r_scbond_it	1.998
r_angle_refined_deg	1.274
r_angle_other_deg	0.946
r_mcangle_it	0.919
r_mcbond_it	0.519
r_symmetry_vdw_other	0.27
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.241
r_symmetry_vdw_refined	0.235
r_nbd_other	0.197
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.173
r_mcbond_other	0.163
r_metal_ion_refined	0.109
r_symmetry_metal_ion_refined	0.089
r_nbtor_other	0.082
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing