3LHN

Crystal structure of putative lipoprotein (NP_718719.1) from Shewanella oneidensis at 1.42 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	1.6000M ammonium sulfate, 0.1M citric acid pH 5.0, 0.001 M copper (II) chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.185	α = 90
b = 50.185	β = 90
c = 300.508	γ = 120

Symmetry
Space Group	P 61 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 325 mm CCD	Flat mirror (vertical focusing)	2009-07-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97932,0.97882	SSRL	BL11-1

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	1.42	28.421	98.7	0.035	18.52			43813		-3	16.807

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	1.42	1.47	94.3		0.492	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	1.42	28.421	43647	2191	99.29	0.173	0.172	0.181	RANDOM	14.711

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]
0.82	0.41		0.82		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.708
r_dihedral_angle_4_deg	12.091
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	5.672
r_scangle_it	3.036
r_mcangle_it	2.027
r_scbond_it	1.881
r_angle_refined_deg	1.772
r_mcbond_it	1.195
r_angle_other_deg	0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.708
r_dihedral_angle_4_deg	12.091
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	5.672
r_scangle_it	3.036
r_mcangle_it	2.027
r_scbond_it	1.881
r_angle_refined_deg	1.772
r_mcbond_it	1.195
r_angle_other_deg	0.91
r_mcbond_other	0.303
r_chiral_restr	0.084
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1622
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.