8PP2 | pdb_00008pp2

Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and native(K86Q) human heavy chain ferritin (Mg formate condition)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CEI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	reservoir: 0.19M Magnesium Formate Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl 2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to coverslide in this order.

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.802	α = 90
b = 126.802	β = 90
c = 175.598	γ = 90

Symmetry
Space Group	P 4

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 EIGER X 16M		2020-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	1.0332	PETRA III, EMBL c/o DESY	P14 (MX2)

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	49.061	99.9	0.173	0.187	0.07	0.998	10.2	13.9		186148

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	2.03			1.164	1.257	0.473	0.824		13.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.001	49.061	186147	9313	99.924	0.205	0.2032	0.21	0.2468	0.25	Random	30.915

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]
-0.816			-0.816		1.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.597
r_dihedral_angle_4_deg	20.745
r_dihedral_angle_3_deg	14.715
r_lrange_other	7.294
r_lrange_it	7.288
r_dihedral_angle_1_deg	6.144
r_scangle_it	4.72
r_scangle_other	4.72
r_mcangle_it	3.413
r_mcangle_other	3.413
r_scbond_it	3.091
r_scbond_other	3.091
r_mcbond_it	2.494
r_mcbond_other	2.491
r_angle_refined_deg	1.509
r_angle_other_deg	1.366
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.192
r_nbd_other	0.187
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.119
r_symmetry_xyhbond_nbd_other	0.097
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17070
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data scaling
xia2	data scaling
MOLREP	phasing