7O64 | pdb_00007o64

Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 1 minute.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R03

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281.15	1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.168	α = 90
b = 184.168	β = 90
c = 184.168	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 PILATUS3 6M		2018-02-19	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-19	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I03	1.73940	Diamond	I03
3	SYNCHROTRON	DIAMOND BEAMLINE I03	1.74380	Diamond	I03

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	1.96	65.11	87.7	0.166	0.172	0.037	0.997	11.3	21		17419		2	20.2

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	1.96	2.07	100		0.672	0.696	0.149	0.949	3.4	21.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1R03	1.96	55.59	16533	803	87.52	0.1647	0.1628	0.16	0.2043	0.21	RANDOM	28.453

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	38.194
r_dihedral_angle_4_deg	18.041
r_dihedral_angle_3_deg	13.575
r_dihedral_angle_1_deg	5.736
r_angle_refined_deg	1.692
r_chiral_restr	0.109
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1407
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.