8A5N

X-ray structure of human H-chain ferritin treated with SDS

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
3.07	59.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.92	α = 90
b = 183.92	β = 90
c = 183.92	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		2022-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.52	106.18	99.5	0.185	0.185	0.016	1	41.2	20		41266

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	1.52	1.55	100		0.859	2.4	15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5N27	1.52	106.18	41266	2056	99.489	0.153	0.1513	0.1903	22.741

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	38.741
r_dihedral_angle_4_deg	20.723
r_dihedral_angle_3_deg	13.037
r_lrange_it	8.141
r_lrange_other	7.75
r_dihedral_angle_1_deg	5.563
r_scangle_it	5.448
r_scangle_other	5.446
r_scbond_it	3.59
r_scbond_other	3.588
r_mcangle_it	3.461
r_mcangle_other	3.445
r_mcbond_it	2.282
r_mcbond_other	2.25
r_angle_refined_deg	1.815
r_angle_other_deg	1.607
r_symmetry_xyhbond_nbd_refined	0.47
r_xyhbond_nbd_refined	0.269
r_nbd_refined	0.254
r_symmetry_xyhbond_nbd_other	0.244
r_nbd_other	0.183
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.176
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.059
r_symmetry_metal_ion_refined	0.015
r_bond_refined_d	0.014
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	355
Heterogen Atoms	27

Software

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