9SGG | pdb_00009sgg

Human UCK1 in complex with NHC and ATP

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		294	Condition C2 of Morpheus Screen: 0.09M NPS, 0.1 M Buffer System 1 pH 6.5, 50 % (v/v) EDO_P8K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.886	α = 90
b = 154.639	β = 98.77
c = 67.568	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 XE 16M		2025-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	2.396	77.32	99.1	0.992	11.5	7.2		51109

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	2.4	2.44			0.387

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	2.396	77.32	51065	2587	99.003	0.209	0.2064	0.2075	0.2535	0.2544	71.415

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]
2.079		-1.184	-0.592		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.617
r_dihedral_angle_6_deg	14.568
r_lrange_it	13.87
r_lrange_other	13.854
r_scangle_it	11.837
r_scangle_other	11.836
r_dihedral_angle_2_deg	11.028
r_mcangle_it	10.128
r_mcangle_other	10.128
r_scbond_it	8.252
r_scbond_other	8.251
r_mcbond_it	7.286
r_mcbond_other	7.283
r_dihedral_angle_1_deg	6.164
r_angle_refined_deg	1.797
r_angle_other_deg	0.606
r_symmetry_xyhbond_nbd_other	0.352
r_chiral_restr_other	0.339
r_dihedral_angle_other_2_deg	0.285
r_nbd_other	0.25
r_xyhbond_nbd_refined	0.236
r_nbd_refined	0.223
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.167
r_ncsr_local_group_3	0.089
r_ncsr_local_group_6	0.087
r_ncsr_local_group_5	0.085
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_2	0.081
r_ncsr_local_group_4	0.068
r_ncsr_local_group_1	0.063
r_symmetry_xyhbond_nbd_refined	0.019
r_bond_refined_d	0.008
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	6784
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
AutoProcess	data reduction
AutoProcess	data scaling
PHASER	phasing