8V36 | pdb_00008v36

Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with NADH

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	7.5	293	HEPES, magnesium chloride, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.307	α = 90
b = 87.556	β = 90
c = 134.197	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		2023-10-27	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	2.235	44.73	99.7	0.049	0.022	1	12.7	6.7		44738

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	2.24	2.31			1.139	0.512	0.752	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.235	43.896	44674	2261	99.639	0.226	0.2226	0.2272	0.2805	0.2825	71.98

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]
5.424			-1.048		-4.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.707
r_dihedral_angle_3_deg	13.322
r_lrange_it	8.967
r_lrange_other	8.967
r_mcangle_it	6.15
r_mcangle_other	6.149
r_dihedral_angle_1_deg	6.132
r_scangle_it	5.891
r_scangle_other	5.89
r_dihedral_angle_2_deg	5.439
r_mcbond_it	3.802
r_mcbond_other	3.802
r_scbond_it	3.544
r_scbond_other	3.543
r_angle_refined_deg	0.92
r_angle_other_deg	0.315
r_nbd_other	0.222
r_nbd_refined	0.205
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.169
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.076
r_metal_ion_refined	0.064
r_dihedral_angle_other_2_deg	0.05
r_chiral_restr	0.042
r_chiral_restr_other	0.007
r_bond_refined_d	0.003
r_gen_planes_refined	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	6268
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	90

Software

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