6TR9 | pdb_00006tr9

Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A

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
3.69	66.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.215	α = 90
b = 151.215	β = 90
c = 151.215	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		2018-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	2.46	75.61	100	0.106	0.112	0.024	1	21.2	21.2		11055		2	50.2

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	2.46	2.59	100		1.044	1.09	0.233	0.929	3.1	21.6

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	2.46	61.81	10926	581	98.869	0.204	0.2005	0.19	0.2579	0.25	47.624

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	35.271
r_dihedral_angle_4_deg	23.051
r_dihedral_angle_3_deg	16.807
r_lrange_it	9.876
r_lrange_other	9.819
r_scangle_it	8.237
r_scangle_other	8.234
r_mcangle_other	6.152
r_mcangle_it	6.148
r_scbond_it	5.834
r_scbond_other	5.83
r_dihedral_angle_1_deg	5.801
r_mcbond_it	4.35
r_mcbond_other	4.339
r_angle_other_deg	2.465
r_angle_refined_deg	1.751
r_symmetry_nbd_refined	0.257
r_metal_ion_refined	0.245
r_nbd_refined	0.229
r_symmetry_metal_ion_refined	0.224
r_symmetry_nbd_other	0.221
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_other	0.208
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.188
r_nbtor_refined	0.184
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.036
r_bond_refined_d	0.014
r_gen_planes_other	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1364
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	7

Software

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