24GH | pdb_000024gh

Crystal structure of HpsK from Bilophila wadsworthia in complex with S-DHPS (2,3-dihydroxypropanesulfonate)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3350, Bis-Tris, pH 5.5, sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.753	α = 70.309
b = 52.048	β = 88.754
c = 66.644	γ = 80.142

Symmetry
Space Group	P 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 EIGER X 16M		2025-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.827	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.05	46.659	94.7	1	11.3	3.6		285217

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.07			0.86

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.05	46.659	285216	14616	94.724	0.119	0.1178	0.1178	0.1361	0.1361	RANDOM	11.197

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]
0.181	0.139	-0.104	0.067	-0.088	-0.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.17
r_dihedral_angle_3_deg	12.121
r_lrange_it	12.108
r_lrange_other	9.853
r_scangle_it	7.435
r_scangle_other	7.435
r_dihedral_angle_2_deg	7.406
r_dihedral_angle_1_deg	6.054
r_scbond_other	5.329
r_scbond_it	5.328
r_mcangle_other	4.439
r_mcangle_it	4.43
r_rigid_bond_restr	4.196
r_mcbond_it	3.221
r_mcbond_other	3.205
r_angle_refined_deg	1.907
r_angle_other_deg	0.674
r_symmetry_nbd_refined	0.3
r_symmetry_xyhbond_nbd_other	0.268
r_nbd_other	0.261
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4981
Nucleic Acid Atoms
Solvent Atoms	857
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing