6TS0 | pdb_00006ts0

Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A Fe(III)-loaded for 30 minutes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LG8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.73	66.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.386	α = 90
b = 151.386	β = 90
c = 151.386	γ = 90

Symmetry
Space Group	I 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	1.73888	Diamond	I03
3	SYNCHROTRON	DIAMOND BEAMLINE I03	1.74478	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
2	2.18	107.34	100	0.088	0.101	0.022	1	21.2	20.1		15908		2	55.9

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)
2	2.18	2.3	100		1.513	1.585	0.351	0.744	2.2	20

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LG8	2.2	47.918	15218	755	98.985	0.206	0.2035	0.2	0.2481	0.25	44.069

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	33.928
r_dihedral_angle_4_deg	24.618
r_dihedral_angle_3_deg	16.076
r_lrange_other	11.424
r_lrange_it	11.418
r_scangle_it	8.915
r_scangle_other	8.915
r_scbond_it	6.478
r_scbond_other	6.473
r_dihedral_angle_1_deg	5.909
r_mcangle_it	5.703
r_mcangle_other	5.703
r_mcbond_it	4.392
r_mcbond_other	4.371
r_angle_other_deg	2.471
r_angle_refined_deg	1.875
r_nbd_other	0.258
r_nbd_refined	0.241
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.189
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.14
r_metal_ion_refined	0.139
r_symmetry_metal_ion_refined	0.122
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.036
r_bond_refined_d	0.015
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1352
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	11

Software

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