24GG | pdb_000024gg

Crystal structure of apo HpsK from Bilophila wadsworthia

X-RAY DIFFRACTION

---

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, Tris, pH 8.5, sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.017	α = 90
b = 87.806	β = 108.841
c = 65.954	γ = 90

Symmetry
Space Group	P 1 21 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	2.01	48.41	98.2	0.99	6.6	7.1		39014

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	2.01	2.06			0.64

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	2.006	35.936	38993	1989	97.995	0.177	0.1747	0.1828	0.2275	0.2318	RANDOM	21.294

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]
0.244		-0.757	1.379		-0.898

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.524
r_dihedral_angle_3_deg	14.002
r_dihedral_angle_2_deg	7.357
r_dihedral_angle_1_deg	6.045
r_lrange_it	4.743
r_lrange_other	4.708
r_scangle_it	3.848
r_scangle_other	3.847
r_scbond_it	2.368
r_scbond_other	2.368
r_mcangle_it	2.127
r_mcangle_other	2.127
r_angle_refined_deg	1.437
r_mcbond_it	1.424
r_mcbond_other	1.424
r_angle_other_deg	0.5
r_nbd_refined	0.217
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.183
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	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	4867
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms

Software

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