4KI3 | pdb_00004ki3

1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	PEG 3350 20% w/v NH4 dihydrogen Phosphate 0.2M, protein at 34 mg/mL, cryo- 20% glycerol+paratone, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.201	α = 94.3
b = 67.13	β = 94.01
c = 132.563	γ = 120.01

Symmetry
Space Group	P 1

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 300 mm CCD	Be-Lenses	2013-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.7	30	94.8	0.091	14.22	4.1	207123	207123		-3	23.3

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	1.7	1.73	95.4		0.598	2.7	4.1	10516

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 (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 3KSN	1.7	29.09	196543	196543	10490	93.77	0.20539	0.20355	0.21	0.23956	0.24	RANDOM	22.516

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]
-12.08	-0.36	0.27	-10.36	-0.37	22.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.931
r_dihedral_angle_4_deg	11.736
r_dihedral_angle_3_deg	8.712
r_scangle_it	4.335
r_scbond_it	2.995
r_dihedral_angle_1_deg	2.637
r_mcangle_it	1.863
r_angle_refined_deg	1.657
r_mcbond_it	1.173
r_angle_other_deg	0.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.931
r_dihedral_angle_4_deg	11.736
r_dihedral_angle_3_deg	8.712
r_scangle_it	4.335
r_scbond_it	2.995
r_dihedral_angle_1_deg	2.637
r_mcangle_it	1.863
r_angle_refined_deg	1.657
r_mcbond_it	1.173
r_angle_other_deg	0.841
r_mcbond_other	0.405
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16593
Nucleic Acid Atoms
Solvent Atoms	1497
Heterogen Atoms	61

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	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.