9P0T | pdb_00009p0t

Structure of PYCR1 complexed with the allosteric inhibitor 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid in a remote site and NADH and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid in the active site

X-RAY DIFFRACTION

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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 400 mM Li2SO4, 13% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 22 mM 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid, 3.5 mM NADH, and 10 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 125 mM 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.54	α = 90
b = 180.592	β = 106.62
c = 88.109	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		2025-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97920	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	1.79	92.59	98.7	0.178	0.193	0.073	0.995	9.2	6.8		307049

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	1.79	1.82		98.1	1.341	1.452	0.551	0.229		6.8

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	1.79	47.71	0.29	307049	15596	98.01	0.1968	0.1954	0.1858	0.223	0.2146

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	12.894
f_angle_d	0.892
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	9876
Nucleic Acid Atoms
Solvent Atoms	894
Heterogen Atoms	382

Software

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