8PP5 | pdb_00008pp5

Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-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	6H6U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	reservoir: 0.19M Magnesium Formate Ftn(pos)-m1: 4 mg/mL in 50mM Tris pH 7.5 0.9 M NaCl 2microliter reservoir + 1microliter Ftn(pos)-m1 +1 microliterL 50mM Tris pH 7.5 0.3 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.898	α = 90
b = 126.898	β = 90
c = 187.468	γ = 90

Symmetry
Space Group	I 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		2021-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97625	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.75	105.09	98.9	0.174	0.193	0.082	0.997	8.3	10.5		145913

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	1.75	1.78			3.671	4.335	2.24	0.184		6.4

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	2	105.086	99602	4906	99.991	0.162	0.1603	0.17	0.1925	0.17	26.449

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]
0.545			0.545		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.117
r_dihedral_angle_3_deg	14.558
r_dihedral_angle_2_deg	9.773
r_lrange_it	7.412
r_lrange_other	7.371
r_scangle_it	6.464
r_scangle_other	6.463
r_dihedral_angle_1_deg	5.605
r_scbond_it	4.165
r_scbond_other	4.165
r_mcangle_it	3.366
r_mcangle_other	3.366
r_mcbond_it	2.39
r_mcbond_other	2.383
r_angle_refined_deg	1.507
r_angle_other_deg	0.514
r_nbd_refined	0.229
r_nbtor_refined	0.185
r_metal_ion_refined	0.182
r_nbd_other	0.178
r_symmetry_nbd_other	0.168
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.12
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8568
Nucleic Acid Atoms
Solvent Atoms	916
Heterogen Atoms	10

Software

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