3FW5 | pdb_00003fw5

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	1.0-1.4M Ammonium sulfate, 50 mM Sodium Chloride, 200 mM Lithium Sulfate, 100 mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.904	α = 90
b = 114.904	β = 90
c = 119.164	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		2008-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	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	2.3	50	99.9	0.048	25	8	67567	35984			45.5

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)
	2.3	2.38	100		0.4	5.39	7.8	3519

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 (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	1L6M	2.3	40.62	32519	3403	99.85	0.24825	0.24398	0.25	0.28973	0.29	RANDOM	35.513

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]
0.22			0.22		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.356
r_dihedral_angle_4_deg	21.478
r_dihedral_angle_3_deg	15.069
r_dihedral_angle_1_deg	5.172
r_scangle_it	1.257
r_angle_refined_deg	0.941
r_angle_other_deg	0.791
r_mcangle_it	0.784
r_scbond_it	0.758
r_mcbond_it	0.418
r_metal_ion_refined	0.236
r_nbd_other	0.181
r_nbtor_refined	0.176
r_nbd_refined	0.163
r_symmetry_vdw_other	0.144
r_symmetry_hbond_refined	0.113
r_symmetry_vdw_refined	0.106
r_xyhbond_nbd_refined	0.094
r_nbtor_other	0.08
r_chiral_restr	0.061
r_mcbond_other	0.038
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3901
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	92

Software

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