3F1Z

Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.46 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	31.0% polyethylene glycol 600, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.42	α = 90
b = 105.507	β = 90
c = 181.25	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

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	2.46	29.881	99.8	0.111	0.111	4.443	7.5		68362			50.365

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	2.46	2.52	99.7		0.696	0.696	1.1	7.6	4955

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	SAD	THROUGHOUT	2.46	29.881	68310	3458	99.71	0.194	0.192	0.228	RANDOM	35.156

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]
-0.67			0.2		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.724
r_dihedral_angle_4_deg	19.472
r_dihedral_angle_3_deg	13.443
r_dihedral_angle_1_deg	3.554
r_mcangle_it	1.718
r_angle_refined_deg	1.698
r_scangle_it	1.515
r_mcbond_it	1.159
r_scbond_it	1.088
r_angle_other_deg	0.932
r_symmetry_vdw_other	0.286
r_mcbond_other	0.276
r_nbd_refined	0.209
r_nbd_other	0.191
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.146
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.098
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9080
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing