9FOD | pdb_00009fod

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

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	6.5	291	0.2M NH4SO4, 0.1M Bis-Tris pH 6.5, 25% w/v PEG3350 300nl drop, mixed either 1:1 or 2:1

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.938	α = 90
b = 94.811	β = 90
c = 95.726	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	1.44	67.36	95.4	0.088	0.999	16.6	13.7		55539

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	1.44	1.57	69.3		1.838	0.741		13.7

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	1.444	67.36	55539	2795	77.25	0.142	0.1403	0.1386	0.1767	0.1747	18.895

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]
-2.609			3.276		-0.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.106
r_dihedral_angle_3_deg	13.302
r_dihedral_angle_2_deg	12.601
r_dihedral_angle_1_deg	6.99
r_rigid_bond_restr	5.652
r_lrange_it	3.782
r_lrange_other	3.587
r_scangle_it	2.936
r_scangle_other	2.874
r_scbond_it	2.14
r_scbond_other	2.109
r_mcangle_it	2.101
r_mcangle_other	2.101
r_angle_refined_deg	1.769
r_mcbond_it	1.483
r_mcbond_other	1.475
r_angle_other_deg	0.624
r_nbd_refined	0.218
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.164
r_nbd_other	0.152
r_symmetry_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.122
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2476
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	10

Software

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