9WOJ | pdb_00009woj

Crystal structure of Human FN3K bound with TDI-017425-NX-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q9H479-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	291	0.2 M ammonium sulfate, 0.1 M tri-sodium citrate (pH 6.1), and 23% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.83	59.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.829	α = 90
b = 110.11	β = 92.772
c = 87.744	γ = 90

Symmetry
Space Group	C 1 2 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 S 9M		2024-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.833	93.875	89.3	0.588	0.635	0.238	0.927	3.9	7		23487

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	2.833	3.129	48.2		1.887	2.031	0.749	0.463		7.3

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.833	93.875	23487	1115	57.635	0.253	0.25258	0.2507	0.2533	0.2909	0.2919	RANDOM	18.63

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]
1.716		0.07	-1.155		-0.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.364
r_dihedral_angle_6_deg	9.165
r_dihedral_angle_1_deg	5.601
r_dihedral_angle_2_deg	2.818
r_lrange_it	1.395
r_lrange_other	1.395
r_angle_refined_deg	0.717
r_mcangle_it	0.409
r_mcangle_other	0.409
r_angle_other_deg	0.279
r_scangle_it	0.243
r_scangle_other	0.243
r_mcbond_it	0.217
r_mcbond_other	0.217
r_nbd_refined	0.181
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.162
r_symmetry_nbd_refined	0.143
r_nbd_other	0.127
r_scbond_it	0.124
r_scbond_other	0.124
r_xyhbond_nbd_refined	0.121
r_symmetry_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.034
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9365
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	178

Software

Software
Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building