3ES3 | pdb_00003es3

Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. The Complex with Gold ions. Ferritin H8-H9x Mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6M	2Z6M; one monomer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	Protein solution (11.0 mG/mL H8 in unbuffered 3.0MM NaN3), 2.5mL of precipitant buffer (0.1 M sodium acetate (PH 4.6), 20%(V/V) isopropanol, 0.2M CaCl2), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. Soaking crystals were performed using a mother liquor (no calcium ions) with the addition of 0.5 mM AuCl3 for one week.

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.564	α = 90
b = 181.564	β = 90
c = 181.564	γ = 90

Symmetry
Space Group	F 4 3 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 270			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.98066	CHESS	A1

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	50	98.8	0.128	14.1	5.1	6736	6736			46.3

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	98.8		0.38	3.2	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	2Z6M; one monomer	2.795	34.942	0.13	6191	229	91.08	0.2237	0.2217	0.27	0.2751	26.062

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]
-5.318			-5.318		-5.318

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.599
f_angle_d	0.918
f_chiral_restr	0.065
f_bond_d	0.006
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1402
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	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.