9HO4 | pdb_00009ho4

Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 6B1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M HEPES pH 7.0 0.8M Potassium Sodium Tartrate

Crystal Properties
Matthews coefficient	Solvent content
3	59.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.253	α = 90
b = 97.253	β = 90
c = 128.105	γ = 120

Symmetry
Space Group	P 63 2 2

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 PILATUS 6M		2023-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.48	84.224	96.8	0.999	33.5	20.5		50815			27.44

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	1.485	1.584	74.5		0.571		21.7

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	1.76	84.224	36124	1728	99.983	0.152	0.1509	0.2347	0.1753	0.2501	24.057

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	-0.272		-0.545		1.767

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	21.09
r_lrange_other	20.698
r_dihedral_angle_6_deg	17.378
r_scangle_it	16.005
r_scangle_other	15.999
r_dihedral_angle_3_deg	12.984
r_scbond_it	11.783
r_scbond_other	11.778
r_mcangle_other	11.628
r_mcangle_it	11.597
r_mcbond_it	8.702
r_mcbond_other	8.679
r_dihedral_angle_1_deg	8.312
r_rigid_bond_restr	3.388
r_angle_refined_deg	1.362
r_angle_other_deg	0.5
r_symmetry_nbd_refined	0.245
r_nbd_other	0.224
r_nbd_refined	0.2
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1875
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing