9E35 | pdb_00009e35

Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with beta-sulfopyruvate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DT2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM TRIS-Cl pH 8.0, 0.4 M LiCl2, 5 mM MgCl2, 1 mM MnCl2, 30-40% PEG 8000 and 10 mM beta-sulfopyruvate. 15 mg/mL PnPEPCK

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.784	α = 90
b = 86.097	β = 90
c = 113.423	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 X 16M		2023-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE 7B2	0.9686	CHESS	7B2

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	1.71	68.6	96.1	0.172	0.179	0.05	0.998	5.7	12.6		72872			27.58

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	1.71	1.77	73.9		2.74	2.855	0.805	0.655	0.26	12.6

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	1.71	68.58	1.33	70331	3464	96.13	0.191	0.189	0.189	0.2292	0.2289	31.78

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	12.3642
f_angle_d	0.7994
f_chiral_restr	0.0511
f_bond_d	0.0067
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4745
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
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.