9SGF | pdb_00009sgf

Human UCK1 in complex with NHC

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
2.65	53.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.546	α = 90
b = 155.093	β = 99.624
c = 67.543	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	2.179	77.547	96.6	0.997	0.6	7.1		65838

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	2.18	2.22			0.442

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	2.179	77.547	65502	3198	96.103	0.211	0.2094	0.2119	0.2495	0.2514	60.621

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]
1.129		-2.323	0.804		-1.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.491
r_dihedral_angle_6_deg	14.771
r_lrange_other	11.525
r_lrange_it	11.515
r_dihedral_angle_2_deg	10.633
r_scangle_it	9.684
r_scangle_other	9.682
r_mcangle_other	8.321
r_mcangle_it	8.318
r_scbond_it	6.718
r_scbond_other	6.717
r_mcbond_it	6.024
r_mcbond_other	6.019
r_dihedral_angle_1_deg	5.896
r_angle_refined_deg	1.797
r_angle_other_deg	0.613
r_nbd_other	0.236
r_nbd_refined	0.215
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.127
r_ncsr_local_group_3	0.094
r_ncsr_local_group_6	0.092
r_ncsr_local_group_2	0.088
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_5	0.08
r_ncsr_local_group_4	0.079
r_ncsr_local_group_1	0.075
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	6863
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	74

Software

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