9WOK | pdb_00009wok

Crystal structure of Human FN3K bound with TDI-017058-FA-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, SITTING DROP	7	291	0.1 M HEPES (pH 7.0) and 2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.5	α = 90
b = 113.5	β = 90
c = 166.02	γ = 90

Symmetry
Space Group	P 43 21 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		2024-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.99999	SPring-8	BL45XU

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	2.45	48.54	100	0.144	0.149	0.039	0.999	20.2	26.8		40564

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	2.45	2.55	100		1.764	1.829	0.484	0.76	2.3	27.3

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	2.45	48.54	40563	2044	99.953	0.189	0.18935	0.187	0.1935	0.2329	0.2322	RANDOM	52.477

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]
-0.179			-0.179		0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.583
r_dihedral_angle_6_deg	14.173
r_lrange_other	10.313
r_lrange_it	10.305
r_dihedral_angle_2_deg	9.422
r_scangle_it	8.169
r_scangle_other	8.168
r_dihedral_angle_1_deg	7.05
r_mcangle_other	5.891
r_mcangle_it	5.887
r_scbond_it	5.4
r_scbond_other	5.399
r_mcbond_it	3.974
r_mcbond_other	3.974
r_angle_refined_deg	1.473
r_angle_other_deg	0.52
r_symmetry_xyhbond_nbd_refined	0.376
r_nbd_refined	0.22
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.157
r_nbd_other	0.132
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.072
r_bond_refined_d	0.006
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	4691
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	157

Software

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