8V35

Crystal structure of HpsN from Cupriavidus pinatubonensis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q46N53-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	HEPES, magnesium chloride, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.032	α = 90
b = 87.767	β = 90
c = 134.8	γ = 90

Symmetry
Space Group	P 21 21 21

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		2023-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.94	44.93	99.9	0.036	0.016	1	15.5	6.8		68501

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.98			1.073	0.476	0.789	1.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.94	43.956	68334	3480	99.947	0.221	0.2188	0.262	57.116

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]
3.294			0.689		-3.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.664
r_dihedral_angle_3_deg	13.486
r_lrange_it	6.714
r_lrange_other	6.712
r_dihedral_angle_1_deg	6.086
r_dihedral_angle_2_deg	4.818
r_scangle_it	4.807
r_scangle_other	4.807
r_mcangle_it	4.446
r_mcangle_other	4.445
r_scbond_it	3.007
r_scbond_other	3.007
r_mcbond_it	2.953
r_mcbond_other	2.952
r_angle_refined_deg	0.988
r_angle_other_deg	0.335
r_nbd_refined	0.208
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.152
r_nbd_other	0.118
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.052
r_chiral_restr	0.047
r_symmetry_nbd_refined	0.026
r_metal_ion_refined	0.016
r_chiral_restr_other	0.013
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6273
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	6

Software

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