9I5F | pdb_00009i5f

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NAD holoenzyme, from Helicobacter pylori

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9FQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	200mM sodium citrate tribasic 20% PEG 3350 (w/v) solution was mixed 4:1:1 or 3:2:1 (protein: reservoir: seeds) in 300nl drops.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.936	α = 90
b = 94.866	β = 90
c = 95.701	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		2023-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.6888	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	1.16	67.37	94.1	0.13	0.997	11.3	13.8		82091

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	1.16	1.31	62.4		1.703	0.833	1.6	13.4

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	1.162	67.37	82089	4194	61.302	0.138	0.1364	0.1368	0.1637	0.1646	13.238

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]
-2.003			2.154		-0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.602
r_lrange_it	15.107
r_lrange_other	13.858
r_dihedral_angle_3_deg	11.376
r_dihedral_angle_2_deg	9.62
r_scangle_it	8.327
r_scangle_other	8.178
r_dihedral_angle_1_deg	7.122
r_scbond_it	5.946
r_scbond_other	5.727
r_mcangle_other	5.202
r_mcangle_it	5.195
r_rigid_bond_restr	4.95
r_mcbond_it	3.557
r_mcbond_other	3.52
r_angle_refined_deg	1.989
r_angle_other_deg	0.843
r_nbd_refined	0.218
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.164
r_nbd_other	0.15
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.075
r_dihedral_angle_other_2_deg	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing