8PP4 | pdb_00008pp4

Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and reduced charge negatively supercharged ferritin variant Ftn(neg)-m3 (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	Human Heavy Chain Ferritin

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	reservoir: 0.19M Magnesium FormateFtn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaClFtn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(neg)-m3 added to coverslide in this order.

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.039	α = 90
b = 127.039	β = 90
c = 176.961	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 EIGER2 X 16M		2021-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.99	49.356	99.9	0.037	0.052	0.037	0.999	12.1	2		188549

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			0.392	0.555	0.392	0.749		2

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.999	49.356	188548	9438	99.872	0.183	0.1814	0.19	0.2207	0.23	34.171

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]
-0.898			-0.898		1.796

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.968
r_dihedral_angle_4_deg	19.79
r_dihedral_angle_3_deg	13.932
r_lrange_other	8.812
r_lrange_it	8.802
r_dihedral_angle_1_deg	5.881
r_scangle_it	5.614
r_scangle_other	5.614
r_scbond_it	3.732
r_scbond_other	3.732
r_mcangle_it	3.642
r_mcangle_other	3.639
r_mcbond_it	2.698
r_mcbond_other	2.693
r_angle_refined_deg	1.546
r_angle_other_deg	1.434
r_nbd_refined	0.219
r_nbd_other	0.206
r_symmetry_nbd_refined	0.203
r_xyhbond_nbd_refined	0.173
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.158
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.079
r_metal_ion_refined	0.078
r_xyhbond_nbd_other	0.047
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17107
Nucleic Acid Atoms
Solvent Atoms	896
Heterogen Atoms	24

Software

Software
Software Name	Purpose
xia2	data scaling
XDS	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement