9VIW | pdb_00009viw

Structure of Thermocrinis minervae double ferritin-like protein (ThmDFLP)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A1M6SI41-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	40% v/v Ethanol, 5% w/v PEG 1000, 0.1 M Phosphate/citrate buffer, pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.955	α = 90
b = 105.16	β = 90.273
c = 89.144	γ = 90

Symmetry
Space Group	P 1 21 1

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		2024-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17UM	0.97918	SSRF	BL17UM

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	2.453	46.503	65.1	0.345	0.374	0.142	0.982	5.1	6.9		28140

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)
	2.453	2.716			1.595	1.72	0.638	0.598	1.4	7.2

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	AF-A0A1M6SI41-F1	2.466	46.546	27917	1321	65.542	0.246	0.2433	0.2435	0.2931	0.29	39.953

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]
-0.745		0.762	0.935		-0.197

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.374
r_lrange_it	10.864
r_lrange_other	10.864
r_dihedral_angle_6_deg	9.429
r_scangle_it	7.81
r_scangle_other	7.809
r_mcangle_it	5.48
r_mcangle_other	5.479
r_scbond_it	4.705
r_scbond_other	4.705
r_dihedral_angle_2_deg	4.035
r_dihedral_angle_1_deg	3.757
r_mcbond_it	3.433
r_mcbond_other	3.433
r_angle_refined_deg	0.546
r_symmetry_xyhbond_nbd_refined	0.388
r_symmetry_nbd_refined	0.334
r_nbd_other	0.331
r_xyhbond_nbd_refined	0.248
r_nbd_refined	0.237
r_symmetry_nbd_other	0.22
r_angle_other_deg	0.19
r_nbtor_refined	0.186
r_metal_ion_refined	0.129
r_symmetry_xyhbond_nbd_other	0.098
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.025
r_bond_refined_d	0.001
r_gen_planes_refined	0.001
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9143
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction