9CP9 | pdb_00009cp9

Crystal structure of DHPS-3-dehydrogenase, HpsN H319A variant from Cupriavidus pinatubonensis in complex with substrate (R-DHPS) 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	PEG 3350, BIS-TRIS, lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.324	α = 90
b = 75.809	β = 117.099
c = 84.674	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		2024-07-05	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	2.01	43.82	99.4	1	7.6	3.9		62003

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	2.01	2.06			0.61	1.2

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	2.013	42.299	61984	2921	99.397	0.168	0.1665	0.176	0.1936	0.2002	29.161

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]
0.088		-0.403	0.143		0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.701
r_dihedral_angle_3_deg	11.696
r_dihedral_angle_2_deg	6.596
r_dihedral_angle_1_deg	6.215
r_lrange_it	4.911
r_lrange_other	4.841
r_scangle_it	3.732
r_scangle_other	3.724
r_mcangle_it	2.325
r_mcangle_other	2.325
r_scbond_it	2.298
r_scbond_other	2.279
r_mcbond_it	1.532
r_mcbond_other	1.531
r_angle_refined_deg	1.245
r_angle_other_deg	0.443
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.173
r_nbd_other	0.161
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.125
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.062
r_dihedral_angle_other_2_deg	0.014
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6572
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	123

Software

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