3HWF | pdb_00003hwf

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam2-hopo

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
2.88	57.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.802	α = 90
b = 114.802	β = 90
c = 118.352	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	3.2	50	100	0.135	22.15	13.6	25061	13667

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)
	3.2	3.3	99.8		0.44	6.9	13.7	1330

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	PDB ENTRY 1L6M	3.2	48	12377	1214	99.71	0.22148	0.21647	0.22	0.27186	0.26	Used same set as previously-determined structure	25.926

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]
-0.28			-0.28		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.647
r_dihedral_angle_4_deg	18.806
r_dihedral_angle_3_deg	18.289
r_dihedral_angle_1_deg	9.761
r_angle_refined_deg	2.953
r_scangle_it	1.449
r_angle_other_deg	1.13
r_scbond_it	0.936
r_mcangle_it	0.802
r_mcbond_it	0.438
r_symmetry_vdw_other	0.215
r_nbd_refined	0.205
r_nbd_other	0.202
r_nbtor_refined	0.193
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.08
r_metal_ion_refined	0.071
r_chiral_restr	0.067
r_mcbond_other	0.05
r_bond_refined_d	0.016
r_bond_other_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3920
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	159

Software

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