9P0V | pdb_00009p0v

Structure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid in a remote site and NADH 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 mM Li2SO4, 12% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 20 mM 7-benzamido-4-hydroxynaphthalene-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, 88 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid, and 15 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.757	α = 90
b = 180.373	β = 106.46
c = 88.206	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 16M		2025-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979200	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	1.8	92.14	99.3	0.098	0.106	0.04	0.999	13.8	6.9		302248

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	1.8	1.83		97.7	2.14	2.319	0.882	0.515		6.7

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	1.8	42.04	0.01	302248	15356	98.73	0.1747	0.1733	0.1696	0.2011	0.1976

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	12.712
f_angle_d	0.867
f_chiral_restr	0.05
f_plane_restr	0.008
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9871
Nucleic Acid Atoms
Solvent Atoms	899
Heterogen Atoms	385

Software

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