3BK5

Crystal structure of putative outer membrane lipoprotein-sorting protein domain from Vibrio parahaemolyticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1M Na acetate, 20% PEG 8000, 0.2M MgCl2, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.157	α = 90
b = 128.874	β = 90
c = 41.968	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315	Mirrors	2007-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97980	APS	19-ID

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	50	99.6	0.161	16.8	7.5	18340	17574			28.45

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	2.07	97.1		0.493	2.1	4.9	1731

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	41.96	17275	17275	937	98.83	0.18147	0.17918	0.22646	RANDOM	30.771

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]
-0.63			-0.72		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.487
r_dihedral_angle_4_deg	22.27
r_dihedral_angle_3_deg	15.228
r_dihedral_angle_1_deg	9.325
r_scangle_it	3.812
r_scbond_it	2.501
r_angle_refined_deg	1.641
r_mcangle_it	1.546
r_mcbond_it	1.002
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.487
r_dihedral_angle_4_deg	22.27
r_dihedral_angle_3_deg	15.228
r_dihedral_angle_1_deg	9.325
r_scangle_it	3.812
r_scbond_it	2.501
r_angle_refined_deg	1.641
r_mcangle_it	1.546
r_mcbond_it	1.002
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.12
r_metal_ion_refined	0.028
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1920
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	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 R01GM133198.