24GE | pdb_000024ge

Crystal structure of HpsK from Ruegeria pomeroyi 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 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.793	α = 90
b = 68.756	β = 120.323
c = 71.377	γ = 90

Symmetry
Space Group	C 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	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	0.954	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	1.65	42.208	99.9	1	16.1	5.2		42559

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	1.65	1.68			1

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	1.65	42.208	42559	2150	99.887	0.142	0.1406	0.1532	0.1639	0.1722	RANDOM	12.41

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]
0.284		-0.417	0.722		-0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.416
r_dihedral_angle_3_deg	10.824
r_dihedral_angle_1_deg	6.367
r_dihedral_angle_2_deg	6.184
r_lrange_it	4.341
r_lrange_other	3.999
r_scangle_it	2.703
r_scangle_other	2.702
r_scbond_it	1.725
r_scbond_other	1.724
r_angle_refined_deg	1.498
r_mcangle_other	1.322
r_mcangle_it	1.319
r_mcbond_it	0.882
r_mcbond_other	0.88
r_angle_other_deg	0.534
r_nbd_refined	0.212
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.183
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.119
r_nbd_other	0.115
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.074
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	21

Software

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