Experiment: 38YX

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans in complex with aminoimidazole 4-carboxamide ribonucleotide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9ZOI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	Berkeley E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME, Overnight soak in 10mM AMZ. plate 21242 A1, Puck: PSL-0411, Cryo: 100 mM sodium citrate tribasic/HCl pH 5.5, 200 mM sodium malonate dibasic pH 5.0, 33% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.804	α = 90
b = 170.975	β = 90
c = 173.286	γ = 90

Symmetry
Space Group	P 21 21 21

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 9M		2026-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9786	NSLS-II	19-ID

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	2.59	47.86	100	0.219	0.228	0.061	0.997	11.2	13.6		62743

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	2.59	2.66		100	1.775	1.847	0.506	0.678		13.1

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	2.59	47.61	1.34	62659	3242	99.97	0.1838	0.181	0.1836	0.2377	0.2357

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	14.422
f_angle_d	1.164
f_chiral_restr	0.061
f_bond_d	0.012
f_plane_restr	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11276
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	90

Software

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