9FQ4 | pdb_00009fq4

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NADP holoenzyme, from Helicobacter pylori, with active site cysteine oxidised to sulfenic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9FL1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.2M NH4SO4, 0.1M Tris pH 8.5, 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.478	α = 90
b = 96.196	β = 90
c = 94.728	γ = 90

Symmetry
Space Group	I 2 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 EIGER2 XE 16M		2023-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.2	38.362	98.8	0.089	1	22.2	23.9		120012

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	87.7		0.737	0.896	2.9	10.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.2	38.362	120008	5943	98.745	0.121	0.1204	0.1192	0.1366	0.1361	12.603

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]
-0.78			0.307		0.474

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.275
r_lrange_it	14.45
r_lrange_other	12.951
r_dihedral_angle_3_deg	10.955
r_scangle_it	9.487
r_scangle_other	9.426
r_dihedral_angle_2_deg	8.962
r_dihedral_angle_1_deg	7.067
r_scbond_it	6.814
r_scbond_other	6.755
r_mcangle_other	5.543
r_mcangle_it	5.526
r_rigid_bond_restr	4.647
r_mcbond_it	3.936
r_mcbond_other	3.862
r_angle_refined_deg	1.963
r_dihedral_angle_other_2_deg	1.936
r_angle_other_deg	0.707
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.21
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.172
r_nbd_other	0.148
r_chiral_restr	0.137
r_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
MoRDa	phasing