8V37 | pdb_00008v37

Crystal structure of HpsN D352A mutant from Cupriavidus pinatubonensis in complex with NAD+

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	7.5	293	HEPES, magnesium chlroide, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.784	α = 90
b = 88.348	β = 90
c = 134.11	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	2.228	44.7	99.8	0.086	0.039	1	10.4	6.7		45320

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	2.23	2.3			1.1195	0.533	0.621

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	2.228	44.213	45255	2302	99.793	0.214	0.2119	0.218	0.258	0.2588	53.069

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]
3.634			-1.191		-2.444

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.919
r_dihedral_angle_3_deg	12.667
r_lrange_it	6.216
r_lrange_other	6.209
r_dihedral_angle_1_deg	6.012
r_dihedral_angle_2_deg	4.287
r_scangle_it	4.122
r_scangle_other	4.121
r_mcangle_it	3.921
r_mcangle_other	3.92
r_scbond_it	2.404
r_scbond_other	2.403
r_mcbond_it	2.332
r_mcbond_other	2.331
r_angle_refined_deg	0.856
r_angle_other_deg	0.297
r_nbd_refined	0.197
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.171
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.083
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.069
r_chiral_restr	0.041
r_chiral_restr_other	0.011
r_symmetry_xyhbond_nbd_other	0.009
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	6317
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	46

Software

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