3ERZ | pdb_00003erz

Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel

X-RAY DIFFRACTION

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 (0.1M sodium acetate (PH 4.6), 20%(v/v) isopropanol, 0.2M CaCl2), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. Soaking experiment performed with mercury ions using the mother liquor without calcium ions.

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.941	α = 90
b = 170.941	β = 90
c = 190.144	γ = 90

Symmetry
Space Group	P 4 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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.98066	NSLS	X29A

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	3.06	29	88	0.144	9.6	4.1	47331	47331			57

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)
	3.06	3.16	91.7		0.37	2.7	4	4847

Refinement

Statistics
Diffraction ID	Structure Solution Method	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)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3.056	28.799	0.12	46176	1895	85.79	0.202	0.199	0.2	0.256	0.19	36.198

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]
0.344			0.344		-0.688

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.636
f_angle_d	1.233
f_chiral_restr	0.086
f_bond_d	0.008
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16836
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	20

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.