9RGI | pdb_00009rgi

X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 6 days with [VIVO(acac)2]

X-RAY DIFFRACTION

---

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		293	0.1 M bicine buffer pH 9.0, 2.0 M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.28	α = 90
b = 183.28	β = 90
c = 183.28	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	1.54	91.808	95.6	0.169	1	22.7	66.6		37529

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	1.54	1.57	100		0.359	0.5	59.3

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	1.543	91.808	36982	1859	94.193	0.177	0.1762	0.1859	0.1979	0.2051	31.166

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	39.116
r_dihedral_angle_4_deg	18.189
r_dihedral_angle_3_deg	13.319
r_lrange_it	8.915
r_lrange_other	8.528
r_scangle_other	6.552
r_scangle_it	6.505
r_dihedral_angle_1_deg	5.502
r_scbond_it	4.702
r_scbond_other	4.485
r_mcangle_it	4.102
r_mcangle_other	4.101
r_mcbond_other	2.812
r_mcbond_it	2.81
r_angle_refined_deg	2.066
r_angle_other_deg	1.531
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_refined	0.179
r_metal_ion_refined	0.177
r_nbtor_refined	0.172
r_symmetry_nbd_other	0.171
r_nbd_other	0.15
r_symmetry_xyhbond_nbd_other	0.119
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.081
r_symmetry_metal_ion_refined	0.039
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
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	244
Heterogen Atoms	63

Software

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