3HWE

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-BisHaCam

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
2.93	58.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.428	α = 90
b = 115.428	β = 90
c = 119.289	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	2.8	50	97.4	0.078	12.6	5.5		19821

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)
	2.8	2.9	96		0.24	4	4.8	1909

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Used previously-determined structure	THROUGHOUT	PDB ENTRY 1L6M	2.8	48.17	17936	1842	97.23	0.23287	0.2276	0.28506	Used same set as previously-determined structure	28.198

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]
0.2			0.2		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.659
r_dihedral_angle_3_deg	16.783
r_dihedral_angle_4_deg	16.081
r_dihedral_angle_1_deg	6.987
r_angle_refined_deg	1.084
r_scangle_it	0.884
r_angle_other_deg	0.84
r_scbond_it	0.526
r_mcangle_it	0.443
r_mcbond_it	0.236
r_nbd_refined	0.19
r_nbd_other	0.185
r_nbtor_refined	0.18
r_symmetry_vdw_other	0.172
r_symmetry_hbond_refined	0.148
r_symmetry_vdw_refined	0.137
r_metal_ion_refined	0.128
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.079
r_chiral_restr	0.062
r_mcbond_other	0.023
r_bond_other_d	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4062
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	198

Software

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