24GD | pdb_000024gd

Crystal structure of apo HpsK from Ruegeria pomeroyi, Crystal form 2

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, Bis-Tris, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.849	α = 90
b = 126.101	β = 117.289
c = 58.834	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		2025-04-13	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	1.9	48.792	99.6	1	11.5	3.5		55825

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	1.9	1.94			0.94

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	1.897	48.792	55792	2874	99.524	0.161	0.1594	0.1702	0.1985	0.2083	RANDOM	16.749

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]
0.993		-0.234	0.984		-1.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.516
r_dihedral_angle_3_deg	11.398
r_dihedral_angle_1_deg	6.393
r_dihedral_angle_2_deg	4.958
r_lrange_it	4.304
r_lrange_other	4.137
r_scangle_other	3.12
r_scangle_it	3.117
r_scbond_it	1.981
r_scbond_other	1.981
r_mcangle_it	1.74
r_mcangle_other	1.74
r_angle_refined_deg	1.461
r_mcbond_it	1.207
r_mcbond_other	1.207
r_angle_other_deg	0.519
r_nbd_refined	0.215
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.182
r_nbd_other	0.15
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.086
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.075
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	5106
Nucleic Acid Atoms
Solvent Atoms	684
Heterogen Atoms	30

Software

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