3CBC | pdb_00003cbc

Crystal structure of Siderocalin (NGAL, Lipocalin 2) Y106F complexed with Ferric Enterobactin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	Ammonium sulfate, Sodium Chloride, Lithium Sulfate, Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.809	α = 90
b = 114.809	β = 90
c = 118.695	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				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	2.17	50	99.9	0.049	12.8	7.7	80222	42605

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	2.17	2.17	99.5		0.41	3	6.1	4165

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	2.17	47.14	38466	4058	99.97	0.23307	0.23065	0.23	0.25637	0.26	RANDOM	30.701

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]
-0.19			-0.19		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.87
r_dihedral_angle_3_deg	13.355
r_dihedral_angle_4_deg	11.03
r_dihedral_angle_1_deg	5.018
r_scangle_it	1.261
r_angle_refined_deg	0.866
r_scbond_it	0.78
r_angle_other_deg	0.775
r_mcangle_it	0.772
r_mcbond_it	0.411
r_nbd_other	0.175
r_nbtor_refined	0.172
r_nbd_refined	0.164
r_symmetry_vdw_other	0.151
r_symmetry_vdw_refined	0.129
r_xyhbond_nbd_refined	0.087
r_symmetry_hbond_refined	0.082
r_nbtor_other	0.077
r_chiral_restr	0.055
r_mcbond_other	0.039
r_metal_ion_refined	0.022
r_bond_other_d	0.006
r_bond_refined_d	0.005
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	4155
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	99

Software

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