6TSX | pdb_00006tsx

Crystal structure of horse L ferritin (HoLf) 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	5LG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	30 mM cadmium nitrate, 1 M ammonium sulfate, 200 mM sodium acetate, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.242	α = 90
b = 181.242	β = 90
c = 181.242	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 EIGER2 X 16M		2019-07-26	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-07-26	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-07-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04
2	SYNCHROTRON	DIAMOND BEAMLINE I04	1.73894	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	2.02	104.64	100	0.056	0.06	0.013	1	30.4	21.7		17298		2	38.7

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	2.02	2.13	100		0.901	0.941	0.199	0.915	3.9	22.2

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	5LG2	2.021	54.706	17294	900	99.971	0.186	0.1844	0.18	0.2211	0.22	41.696

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	32.853
r_dihedral_angle_4_deg	18.835
r_dihedral_angle_3_deg	15.599
r_lrange_it	10.183
r_lrange_other	9.866
r_scangle_it	9.189
r_scangle_other	9.184
r_scbond_it	6.466
r_scbond_other	6.462
r_dihedral_angle_1_deg	5.16
r_mcangle_it	4.211
r_mcangle_other	4.208
r_mcbond_other	3.477
r_mcbond_it	3.474
r_angle_other_deg	2.4
r_angle_refined_deg	1.907
r_nbd_refined	0.246
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.184
r_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.15
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.132
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.036
r_bond_refined_d	0.014
r_gen_planes_other	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1348
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	21

Software

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