3BY0 | pdb_00003by0

Crystal structure of Siderocalin (NGAL, Lipocalin 2) W79A-R81A complexed with Ferric Enterobactin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L6M	PDB ENTRY 1L6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.358	α = 90
b = 114.358	β = 90
c = 119.042	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	RIGAKU RAXIS IV		2005-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.572	28.59	100	0.078	0.289	12.6	25655	23194			63.391

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	2.572	2.66	100		0.397	7.1	12.5	2519

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	Used previously-determined structure	THROUGHOUT	PDB ENTRY 1L6M	2.572	28.59	25655	23194	2410	99.72	0.24891	0.24751	0.25	0.26249	0.27	Used same set as previously-determined structure	46.342

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]
0.47			0.47		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.195
r_dihedral_angle_4_deg	17.843
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	4.795
r_scangle_it	0.991
r_angle_refined_deg	0.84
r_angle_other_deg	0.82
r_scbond_it	0.668
r_mcangle_it	0.582
r_mcbond_it	0.456
r_metal_ion_refined	0.213
r_nbd_other	0.207
r_symmetry_vdw_other	0.188
r_nbtor_refined	0.177
r_nbd_refined	0.176
r_xyhbond_nbd_refined	0.111
r_symmetry_vdw_refined	0.101
r_mcbond_other	0.09
r_nbtor_other	0.078
r_symmetry_hbond_refined	0.071
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_bond_other_d	0.006
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4162
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling