8QWA

Adenylosuccinate Synthetase from H. pylori in complex with PLP and IMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PVO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	8.5	285	85mM Tris-HCl pH 8,5 21% PEG4k 170 mM Li2SO4 15% GOL

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.897	α = 90
b = 61.124	β = 98.905
c = 119.254	γ = 90

Symmetry
Space Group	I 1 2 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	CCD	AGILENT ATLAS CCD		2023-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION SUPERNOVA	1.54184

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	1.85	29.821	100	0.047	0.049	0.014	1	48	23.5		41958

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	1.85	1.89			0.24	0.261	0.102	0.991		12.7

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	1.85	29.821	41870	4135	99.752	0.17	0.1669	0.1606	0.2011	0.193	18.619

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]
-0.066		0.738	0.14		-0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.421
r_dihedral_angle_3_deg	13.008
r_dihedral_angle_1_deg	7.601
r_lrange_it	6.26
r_lrange_other	6.186
r_dihedral_angle_2_deg	5.865
r_scangle_it	5.199
r_scangle_other	5.198
r_scbond_it	3.392
r_scbond_other	3.391
r_mcangle_it	2.763
r_mcangle_other	2.763
r_angle_refined_deg	1.963
r_mcbond_it	1.931
r_mcbond_other	1.892
r_angle_other_deg	0.66
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.224
r_symmetry_nbd_other	0.19
r_nbd_other	0.188
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.105
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3176
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing