8A2L

X-ray structure of TRIL-encapsulated human heavy chain ferritin

X-RAY DIFFRACTION

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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	59.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.06	α = 90
b = 183.06	β = 90
c = 183.06	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		2022-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0001	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	105.69	99.9	0.2	0.059	0.998	0.711	20		12183

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100		1.8	1	0.371	0.827		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	2.301	105.69	12183	603	99.787	0.173	0.1706	0.2236	34.08

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	39.756
r_dihedral_angle_4_deg	18.124
r_dihedral_angle_3_deg	13.902
r_lrange_it	9.044
r_lrange_other	9.04
r_scangle_it	6.038
r_scangle_other	6.037
r_dihedral_angle_1_deg	5.896
r_mcangle_it	4.85
r_mcangle_other	4.799
r_scbond_it	3.715
r_scbond_other	3.713
r_mcbond_it	3.017
r_mcbond_other	2.953
r_angle_refined_deg	1.422
r_angle_other_deg	1.386
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.187
r_symmetry_nbd_other	0.178
r_nbd_other	0.167
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.126
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_metal_ion_refined	0.031
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
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	171
Heterogen Atoms	13

Software

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