3PEC | pdb_00003pec

Siderocalin Recognitin of Carboxymycobactins: Interference by the immune system in intracellular iron acquisition by Mycobacteria tuberculosis

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	298	1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.15	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 114.2	β = 90
c = 119.3	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		2009-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	100			77333	41091

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	2.2	2.28	100		0.35	5.6	7	4024

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	Used previously-determined structure	THROUGHOUT	PDB entry 1L6M	2.19	40.66	41091	37100	3912	99.95	0.24783	0.24522	0.26	0.27294	0.29	RANDOM	44.53

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]
-0.15			-0.15		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.36
r_dihedral_angle_4_deg	15.609
r_dihedral_angle_3_deg	13.032
r_dihedral_angle_1_deg	4.717
r_angle_refined_deg	0.97
r_angle_other_deg	0.86
r_scangle_it	0.828
r_scbond_it	0.463
r_mcangle_it	0.359
r_mcbond_it	0.186

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.36
r_dihedral_angle_4_deg	15.609
r_dihedral_angle_3_deg	13.032
r_dihedral_angle_1_deg	4.717
r_angle_refined_deg	0.97
r_angle_other_deg	0.86
r_scangle_it	0.828
r_scbond_it	0.463
r_mcangle_it	0.359
r_mcbond_it	0.186
r_chiral_restr	0.111
r_mcbond_other	0.022
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4005
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	114

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.