3CMP | pdb_00003cmp

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

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	0.2M Ammonium sulfate, 30% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.908	α = 90
b = 114.908	β = 90
c = 118.832	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	2.8	82.48	99	0.077	29.85	9.8	20269	20066

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	2.8	2.9	99.5		0.405	5.92	9.9	1955

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1L6M	2.8	47.96	20269	19017	1026	99.02	0.25108	0.24827	0.25	0.30397	0.3	Used same set as previously-determined structure	31.185

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]
-0.11			-0.11		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.074
r_dihedral_angle_4_deg	17.145
r_dihedral_angle_3_deg	14.554
r_dihedral_angle_1_deg	7.937
r_angle_refined_deg	0.941
r_scangle_it	0.885
r_angle_other_deg	0.792
r_mcangle_it	0.541
r_scbond_it	0.529
r_mcbond_it	0.286
r_nbd_other	0.18
r_nbtor_refined	0.177
r_nbd_refined	0.168
r_symmetry_vdw_refined	0.152
r_symmetry_vdw_other	0.125
r_symmetry_hbond_refined	0.109
r_xyhbond_nbd_refined	0.097
r_nbtor_other	0.078
r_chiral_restr	0.056
r_mcbond_other	0.03
r_metal_ion_refined	0.028
r_bond_other_d	0.007
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3911
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	161

Software

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