9RGJ | pdb_00009rgj

X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 24 h 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
3.06	59.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.71	α = 90
b = 183.71	β = 90
c = 183.71	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	1.498	92.024	93.4	0.2	0.999	20.9	68.1		40254

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	1.5	1.52	81.1		0.326		48.7

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	1.498	92.024	40089	2001	92.969	0.165	0.163	0.1727	0.1958	0.2009	24.824

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	40.289
r_dihedral_angle_4_deg	20.615
r_dihedral_angle_3_deg	13.942
r_lrange_it	9.697
r_lrange_other	9.419
r_dihedral_angle_1_deg	6.875
r_scangle_other	6.286
r_scangle_it	6.192
r_mcangle_it	4.283
r_mcangle_other	4.275
r_scbond_it	4.25
r_scbond_other	4.014
r_mcbond_it	2.797
r_mcbond_other	2.789
r_angle_refined_deg	2.117
r_angle_other_deg	1.616
r_nbd_refined	0.254
r_metal_ion_refined	0.239
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_other	0.181
r_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.173
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1424
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	64

Software

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