4MH6 | pdb_00004mh6

2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	295	Protein: 2.28 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JCSG+ (C9), 0.1M Sodium/Potasium phosphate pH 6.2, 25% (v/v) 1,2 Propanediol, 10% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.114	α = 90
b = 149.114	β = 90
c = 63.422	γ = 90

Symmetry
Space Group	I 41 2 2

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	2013-08-20	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	2.8	30	99.9	0.139	18.3	9.6	9084	9084		-3	55.3

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	2.8	2.85	100		0.603	4.2	10	436

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.8	29.24	8645	8645	434	99.69	0.19195	0.18946	0.1917	0.24308	0.2407	RANDOM	52.031

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]
0.46			0.46		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.165
r_dihedral_angle_4_deg	13.841
r_dihedral_angle_3_deg	11.605
r_long_range_B_refined	8.74
r_long_range_B_other	8.69
r_scangle_other	5.917
r_mcangle_it	4.262
r_mcangle_other	4.26
r_scbond_it	3.759
r_scbond_other	3.553
r_mcbond_it	2.496
r_mcbond_other	2.468
r_dihedral_angle_1_deg	1.935
r_angle_refined_deg	1.649
r_angle_other_deg	0.718
r_chiral_restr	0.085
r_gen_planes_refined	0.019
r_gen_planes_other	0.017
r_bond_refined_d	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1347
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	10

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling