9PG6 | pdb_00009pg6

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q7VZB9-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD added to the protein prior to crystallization. plate 19841 well A1 drop 2, Puck: PSL-2110, Cryo: 80% crystallant + 20% PEG 200

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.826	α = 90
b = 130.061	β = 90.86
c = 140.967	γ = 90

Symmetry
Space Group	P 1 21 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 XE 9M		2025-04-25	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	2.15	49.03	99.8	0.184	0.199	0.075	0.996	7.8	7		153901

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	2.15	2.21		99.7	1.251	1.346	0.495	0.742		7.2

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	2.15	49.03	1.35	153627	7773	99.66	0.1947	0.1928	0.1994	0.2297	0.2328

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	13.172
f_angle_d	0.763
f_chiral_restr	0.05
f_plane_restr	0.008
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20351
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	357

Software

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