8PP3 | pdb_00008pp3

Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and crystal contact tuned negatively supercharged ferritin variant Ftn(neg)-m1 (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 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(Wildtype) added to coverslide in this order.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.007	α = 90
b = 127.007	β = 90
c = 175.193	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 CdTe 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)	0.97625	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	72.1	97.7	0.161	0.046	0.997	8.3	12.1		391240

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58			0.135		5.7

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	1.55	59.774	391211	16135	97.689	0.22	0.2185	0.23	0.2413	0.25	24.427

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]
-0.518			-0.518		1.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.027
r_dihedral_angle_4_deg	18.649
r_dihedral_angle_3_deg	12.733
r_dihedral_angle_1_deg	5.824
r_lrange_it	4.742
r_lrange_other	4.733
r_scangle_it	3.973
r_scangle_other	3.973
r_scbond_it	2.621
r_scbond_other	2.621
r_mcangle_it	2.213
r_mcangle_other	2.211
r_mcbond_it	1.687
r_mcbond_other	1.685
r_angle_refined_deg	1.471
r_angle_other_deg	1.399
r_nbd_refined	0.21
r_nbd_other	0.177
r_symmetry_nbd_refined	0.175
r_symmetry_nbd_other	0.166
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.106
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.067
r_metal_ion_refined	0.032
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	17100
Nucleic Acid Atoms
Solvent Atoms	976
Heterogen Atoms	38

Software

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