24GC | pdb_000024gc

Crystal structure of apo HpsK from Ruegeria pomeroyi, crystal form 1

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, HANGING DROP		293	PEG3350, sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.02	α = 72.289
b = 58.87	β = 70.895
c = 67.7	γ = 62.75

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		2025-04-13	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	1.47	46.83	96.2	1	18.5	3.9		112178

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	1.47	1.5			0.93

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	1.472	46.826	112178	5558	96.147	0.132	0.1305	0.1372	0.1598	0.1619	RANDOM	18.395

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]
-1.266	3.48	-6.725	0.422	1.997	0.845

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.454
r_lrange_it	13.287
r_lrange_other	11.483
r_dihedral_angle_3_deg	11.193
r_dihedral_angle_2_deg	8.721
r_scangle_it	7.85
r_scangle_other	7.849
r_dihedral_angle_1_deg	6.094
r_mcangle_it	5.859
r_mcangle_other	5.859
r_scbond_it	5.439
r_scbond_other	5.438
r_mcbond_it	4.084
r_mcbond_other	4.082
r_rigid_bond_restr	2.618
r_angle_refined_deg	1.494
r_symmetry_xyhbond_nbd_other	0.661
r_angle_other_deg	0.556
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.181
r_symmetry_nbd_refined	0.174
r_nbd_other	0.162
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.076
r_gen_planes_refined	0.008
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	5114
Nucleic Acid Atoms
Solvent Atoms	815
Heterogen Atoms	7

Software

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