9Q46 | pdb_00009q46

Ternary complex of PYCR1 with the allosteric inhibitor 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid in two remote sites and the active site, and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid in the active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TCX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Resevoir contained 340-400 mM Li2SO4, 12-17% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 21 mM 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid and 10 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 50 mM 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.772	α = 90
b = 180.308	β = 106.52
c = 88.14	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		2025-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	1.75	90.15	99.2	0.163	0.177	0.067	0.995	7.9	6.9		325584

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	1.75	1.78		99.8	1.555	1.683	0.637	0.302		6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.75	45.75	0.1	325584	6466	98.71	0.1991	0.1987	0.1924	0.2166	0.2114

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.226
f_angle_d	0.852
f_chiral_restr	0.049
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9695
Nucleic Acid Atoms
Solvent Atoms	865
Heterogen Atoms	221

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing