3K3L | pdb_00003k3l

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin

X-RAY DIFFRACTION

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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
3.15	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 114.2	β = 90
c = 119.3	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	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2.62	50	100	0.057	50.3	12.9	44579	23965

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)
	2.62	2.7	100		0.41	7.51	13.2	2347

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 (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	2.62	41.25	21664	2245	99.94	0.26395	0.25955	0.26	0.3071	0.3	RANDOM	36.449

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.416
r_dihedral_angle_4_deg	20.422
r_dihedral_angle_3_deg	15.346
r_dihedral_angle_1_deg	5.356
r_scangle_it	1.463
r_angle_refined_deg	0.906
r_scbond_it	0.824
r_mcangle_it	0.813
r_angle_other_deg	0.774
r_mcbond_it	0.428
r_chiral_restr	0.056
r_mcbond_other	0.042
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3682
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	128

Software

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