3HWD

Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A-K134A mutant complexed with Ferric Enterobactin

X-RAY DIFFRACTION

---

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	0.2M lithium sulfate, 20% PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.825	α = 90
b = 115.825	β = 90
c = 119.316	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	2.95	50	91	0.084	25.3	8.7	29078	16029

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)
	2.95	3.1	93.7		0.36	5.8	8.6	1613

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	2.95	50	15193	808	90.85	0.2595	0.25727	0.30292	Used same set as previously-determined structure	34.763

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]
0.25			0.25		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.29
r_dihedral_angle_4_deg	17.971
r_dihedral_angle_3_deg	14.689
r_dihedral_angle_1_deg	4.409
r_scangle_it	0.856
r_angle_refined_deg	0.829
r_angle_other_deg	0.792
r_mcangle_it	0.645
r_scbond_it	0.501
r_mcbond_it	0.345
r_nbtor_refined	0.177
r_nbd_other	0.173
r_nbd_refined	0.167
r_symmetry_vdw_refined	0.123
r_symmetry_vdw_other	0.123
r_xyhbond_nbd_refined	0.104
r_nbtor_other	0.077
r_symmetry_hbond_refined	0.058
r_chiral_restr	0.057
r_mcbond_other	0.033
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3865
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	7

Software

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