9CP8 | pdb_00009cp8

Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with product (R-sulfolactate) and NADH

X-RAY DIFFRACTION

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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		293	PEG3350, BIS-TRIS, lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.078	α = 90
b = 75.592	β = 117.279
c = 84.995	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		2024-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95372	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	1.57	41.51	99.4	1	13.9	3.8		129685

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	1.57	1.6			0.9	2.4

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	1.57	37.88	129663	6496	99.402	0.151	0.1495	0.1613	0.1758	0.1852	19.699

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]
-0.811		-0.525	1.071		0.184

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.292
r_dihedral_angle_3_deg	10.453
r_dihedral_angle_2_deg	6.37
r_dihedral_angle_1_deg	6.25
r_lrange_it	4.592
r_lrange_other	4.398
r_scangle_it	3.53
r_scangle_other	3.53
r_scbond_other	2.249
r_scbond_it	2.248
r_mcangle_it	1.974
r_mcangle_other	1.974
r_angle_refined_deg	1.543
r_mcbond_it	1.387
r_mcbond_other	1.387
r_angle_other_deg	0.553
r_nbd_refined	0.224
r_symmetry_nbd_other	0.181
r_nbd_other	0.181
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.077
r_metal_ion_refined	0.056
r_dihedral_angle_other_2_deg	0.013
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6595
Nucleic Acid Atoms
Solvent Atoms	798
Heterogen Atoms	110

Software

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