8GY1

Crystal structure of Ag+ binding to Dendrorhynchus zhejiangensis ferritin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291.15	DzFer crystals were grown in 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v PEG monomethyl ether 2000, followed by soaking for 10 min with 20% glycerol and 100 mM AgNO3.

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.212	α = 90
b = 148.212	β = 90
c = 148.212	γ = 90

Symmetry
Space Group	I 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	PIXEL	DECTRIS EIGER2 X 9M		2022-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL17B	0.979	NFPSS	BL17B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.9	106.78	99.7	0.99	7.2	11.3		21003

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2			0.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	104.8	21003	1107	99.95	0.15273	0.1508	0.16	0.18965	0.2	RANDOM	35.17

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.613
r_dihedral_angle_4_deg	16.748
r_dihedral_angle_3_deg	14.023
r_long_range_B_refined	8.426
r_long_range_B_other	8.348
r_scangle_other	7.539
r_dihedral_angle_1_deg	5.302
r_scbond_it	5.209
r_scbond_other	5.169
r_mcangle_other	3.925
r_mcangle_it	3.913
r_mcbond_it	2.904
r_mcbond_other	2.822
r_angle_refined_deg	1.875
r_angle_other_deg	1.098
r_chiral_restr	0.135
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1366
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
autoPROC	data scaling
BALBES	phasing