9P1B | pdb_00009p1b

P. putida mandelate racemase co-crystallized with tavaborole

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VIM	chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Reservoir solution: PEG3350 (9% w/v), HEPES (50mM; pH 8.0) Protein solution: mandelate racemase (10 mg/ml) + 500uM Tavaborole in 100mM HEPES, pH 7.5, 3.3mM MgCl2 2 uL of protein solution was mixed with 2 uL of well solution. Cube-like crystals grew spontaneously over 18-25 days. Crystals were equilibrated in synthetic stabilizing solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 5% v/v ethylene glycol) for 5 minutes and then transferred directly to cryoprotectant solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 20% v/v ethylene glycol) for 5 minutes prior to flash freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.646	α = 90
b = 150.646	β = 90
c = 177.551	γ = 90

Symmetry
Space Group	I 4 2 2

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 PILATUS 6M		2025-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.618	114.87	85.6	0.24	0.249	0.063	0.995	7.2	14.5		81806			8.45

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	1.618	1.833	42		0.598	0.655	0.257	0.769	1.6	5.9

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	57.44	1.33	79181	3977	84.31	0.2018	0.2	0.2022	0.2348	0.2352	11.39

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	15.6158
f_angle_d	1.043
f_chiral_restr	0.0611
f_bond_d	0.0113
f_plane_restr	0.0092

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5390
Nucleic Acid Atoms
Solvent Atoms	652
Heterogen Atoms	44

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.