7O6C | pdb_00007o6c

Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 15 minutes under anaerobic environment

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
3.07	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.449	α = 90
b = 182.449	β = 90
c = 182.449	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-F		2019-05-17	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-05-17	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-05-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.87000	Diamond	I04
2	SYNCHROTRON	DIAMOND BEAMLINE I04	1.73892	Diamond	I04
3	SYNCHROTRON	DIAMOND BEAMLINE I04	1.75120	Diamond	I04

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	1.2	55.01	100	0.066	0.07	0.015	1	22	20.1		81103		2	9.9

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	1.2	1.26	100		0.76	0.817	0.215	0.869	3.3	14.1

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	1.2	52.72	76990	4101	99.97	0.1222	0.1212	0.12	0.1425	0.14	RANDOM	13.691

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	38.35
r_dihedral_angle_4_deg	12.358
r_dihedral_angle_3_deg	12.119
r_dihedral_angle_1_deg	5.34
r_rigid_bond_restr	1.684
r_angle_other_deg	1.591
r_angle_refined_deg	1.469
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.35
r_dihedral_angle_4_deg	12.358
r_dihedral_angle_3_deg	12.119
r_dihedral_angle_1_deg	5.34
r_rigid_bond_restr	1.684
r_angle_other_deg	1.591
r_angle_refined_deg	1.469
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1403
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	25

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.