6TSJ | pdb_00006tsj

Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 15 minutes

X-RAY DIFFRACTION

---

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
3.7	66.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.907	α = 90
b = 151.907	β = 90
c = 151.907	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	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.07227	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	2.3	48.04	100	0.086	0.091	0.02	1	23.9	21.3		13632		2	47.7

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	2.3	2.42	100		1.041	1.089	0.232	0.901	3.3	21.7

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	2.3	43.89	13623	670	99.956	0.198	0.1952	0.19	0.2623	0.25	47.514

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	35.853
r_dihedral_angle_4_deg	25.931
r_dihedral_angle_3_deg	16.699
r_lrange_it	12.232
r_lrange_other	12.212
r_scangle_it	10.182
r_scangle_other	10.182
r_scbond_it	7.266
r_scbond_other	7.261
r_mcangle_it	6.25
r_mcangle_other	6.247
r_dihedral_angle_1_deg	5.581
r_mcbond_other	4.5
r_mcbond_it	4.499
r_angle_other_deg	2.479
r_angle_refined_deg	1.909
r_nbd_refined	0.241
r_nbd_other	0.237
r_symmetry_nbd_other	0.223
r_nbtor_refined	0.185
r_chiral_restr	0.182
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.101
r_metal_ion_refined	0.08
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.036
r_symmetry_metal_ion_refined	0.019
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	1380
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	12

Software

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