6TSA | pdb_00006tsa

Crystal structure of human L ferritin (HuLf) 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
3.76	67.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.69	α = 90
b = 152.69	β = 90
c = 152.69	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 PILATUS 6M-F		2017-12-12	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2017-12-12	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2017-12-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.07227	ESRF	ID29
2	SYNCHROTRON	ESRF BEAMLINE ID29	1.73769	ESRF	ID29
3	SYNCHROTRON	ESRF BEAMLINE ID29	1.74502	ESRF	ID29

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	2.18	48.28	100	0.122	0.128	0.028	0.999	13.6	21.3		16176		2	47.2

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	2.18	2.3	100		1.573	1.641	0.347	0.839	2.2	22.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LG8	2.18	48.28	16074	825	99.369	0.205	0.2021	0.2	0.2575	0.27	47.655

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	34.428
r_dihedral_angle_4_deg	24.294
r_dihedral_angle_3_deg	17.05
r_lrange_it	11.01
r_lrange_other	10.855
r_scangle_other	9.196
r_scangle_it	9.191
r_scbond_it	6.99
r_scbond_other	6.985
r_mcangle_other	6.228
r_mcangle_it	6.223
r_dihedral_angle_1_deg	5.564
r_mcbond_it	4.641
r_mcbond_other	4.615
r_angle_other_deg	2.445
r_angle_refined_deg	1.796
r_symmetry_nbd_refined	0.33
r_nbd_refined	0.246
r_symmetry_xyhbond_nbd_refined	0.229
r_symmetry_nbd_other	0.212
r_nbd_other	0.191
r_nbtor_refined	0.187
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.171
r_metal_ion_refined	0.119
r_symmetry_nbtor_other	0.075
r_bond_other_d	0.036
r_bond_refined_d	0.014
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1376
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	20

Software

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