4ZHG | pdb_00004zhg

Siderocalin-mediated recognition and cellular uptake of actinides

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4	298	NaCl, Li2SO4, Acetate, Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.733	α = 90
b = 117.693	β = 90
c = 121.225	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2014-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	50	99.1	0.114	0.127	0.056	11.1	4.8		96900

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	81.7		0.348	0.401	0.196	0.865		3.6	3939

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	MOLECULAR REPLACEMENT	THROUGHOUT	1LM6	2.05	50	91974	4848	99.52	0.1961	0.195	0.2	0.2167	0.22	RANDOM	26.441

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]
0.32			0.04		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.078
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_3_deg	14.631
r_dihedral_angle_1_deg	7.704
r_mcangle_it	2.951
r_mcbond_it	1.989
r_mcbond_other	1.989
r_angle_refined_deg	1.188
r_angle_other_deg	0.844
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.078
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_3_deg	14.631
r_dihedral_angle_1_deg	7.704
r_mcangle_it	2.951
r_mcbond_it	1.989
r_mcbond_other	1.989
r_angle_refined_deg	1.188
r_angle_other_deg	0.844
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8496
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	363

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.