6KP5 | pdb_00006kp5

crystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia pestis in P21212 space group with sulphate ions in the active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XTK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.2M Lithium sulphate, 0.1M Tris:HCl pH 8.5, 1.26M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.32	α = 90
b = 94.63	β = 90
c = 51.67	γ = 90

Symmetry
Space Group	P 21 21 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		2018-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.97620	ELETTRA	11.2C

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	1.1	47.32	99.9	0.112	0.117	0.035	0.998	10.4	11.3		116357

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	1.1	1.12	99.7		1.077	1.13	0.338	0.829		10.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5XTK	1.1	47.315	110114	5934	99.6	0.163	0.1618	0.17	0.1864	0.2	RANDOM	12.589

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]
-2.36			1.32		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.165
r_dihedral_angle_4_deg	13.841
r_dihedral_angle_3_deg	13.187
r_dihedral_angle_1_deg	6.664
r_rigid_bond_restr	6.535
r_angle_refined_deg	2.153
r_angle_other_deg	1.602
r_chiral_restr	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.165
r_dihedral_angle_4_deg	13.841
r_dihedral_angle_3_deg	13.187
r_dihedral_angle_1_deg	6.664
r_rigid_bond_restr	6.535
r_angle_refined_deg	2.153
r_angle_other_deg	1.602
r_chiral_restr	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2139
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	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.