9PVT | pdb_00009pvt

Crystal structure of HpsO in complex with HAS (hydroxyacetonesulfonate) from Cupriavidus pinatubonensis

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	0.1 M Tris-HCl (pH 8.0), 0.2 M NaCl or LiCl, 20-22% (w/v) PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.121	α = 90
b = 124.8	β = 117.325
c = 51.47	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		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)	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	1.55	46.783	99.1	1	8.8	3.4		64293

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	1.55	1.58			0.61

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.55	46.783	64292	3267	99.074	0.163	0.162	0.174	0.1842	0.1926	33.067

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]
-0.658		-0.346	0.767		0.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.012
r_dihedral_angle_3_deg	12.317
r_dihedral_angle_1_deg	6.672
r_dihedral_angle_2_deg	5.73
r_lrange_it	4.694
r_lrange_other	4.642
r_scangle_it	2.989
r_scangle_other	2.988
r_scbond_it	1.93
r_scbond_other	1.93
r_mcangle_it	1.795
r_mcangle_other	1.795
r_angle_refined_deg	1.519
r_mcbond_it	1.213
r_mcbond_other	1.213
r_dihedral_angle_other_2_deg	1.002
r_angle_other_deg	0.539
r_nbd_refined	0.223
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.177
r_nbd_other	0.164
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3611
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	122

Software

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