9RGH | pdb_00009rgh

X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated overnight with [VIVO(acac)2]

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	2.0 M magnesium chloride, 0.1 M bicine buffer pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.99	α = 90
b = 182.99	β = 90
c = 182.99	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	PIXEL	DECTRIS PILATUS 6M		2024-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.38	105.65	94.4	0.136	1	25.7	61.9		50886

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	1.38	1.41	100		0.399	0.6	61.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.383	105.649	50390	2511	93.483	0.162	0.1609	0.1686	0.1767	0.1701	22.965

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	41.142
r_dihedral_angle_4_deg	21.409
r_dihedral_angle_3_deg	12.908
r_lrange_it	8.616
r_lrange_other	8.319
r_scangle_other	6.426
r_scangle_it	6.241
r_dihedral_angle_1_deg	5.315
r_scbond_other	4.204
r_scbond_it	4.156
r_mcangle_it	4.003
r_mcangle_other	4.002
r_mcbond_it	2.472
r_mcbond_other	2.471
r_angle_refined_deg	2.332
r_angle_other_deg	1.61
r_xyhbond_nbd_refined	0.261
r_nbd_refined	0.258
r_symmetry_nbd_refined	0.255
r_metal_ion_refined	0.194
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.173
r_symmetry_nbd_other	0.172
r_symmetry_xyhbond_nbd_other	0.155
r_nbd_other	0.145
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.087
r_symmetry_metal_ion_refined	0.036
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1424
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing