9R1S | pdb_00009r1s

Crystal structure of an NtA622L variant in complex with NADPH and Nicotinic acid N-glucoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previously solved structure with a different ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.05 M BIS-TRIS, 12.5% w/v Polyethylene glycol 3,350, 5 mg/ml protein, 1 mM Nicotinic acid N-glucoside

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.697	α = 110.028
b = 45.076	β = 94.801
c = 46.471	γ = 112.579

Symmetry
Space Group	P 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 9M		2024-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	1.5	38.02	80.5	0.994	4	1.8		39296

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	1.5	1.53			0.89

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	1.5	38.015	39295	1935	80.509	0.201	0.1986	0.2137	0.2425	0.2495	34.361

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]
-2.248	1.618	0.228	3.12	1.298	-3.347

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	37.489
r_lrange_other	35.082
r_dihedral_angle_6_deg	15.831
r_dihedral_angle_3_deg	15.528
r_mcangle_it	15.337
r_mcangle_other	15.337
r_scangle_it	12.73
r_scangle_other	12.726
r_dihedral_angle_2_deg	12.018
r_mcbond_it	11.298
r_mcbond_other	11.291
r_rigid_bond_restr	9.438
r_scbond_other	9.146
r_scbond_it	9.144
r_dihedral_angle_other_2_deg	7.914
r_dihedral_angle_1_deg	7.324
r_angle_refined_deg	2.263
r_angle_other_deg	1.044
r_symmetry_xyhbond_nbd_other	0.208
r_nbd_refined	0.181
r_nbtor_refined	0.152
r_symmetry_nbd_other	0.134
r_nbd_other	0.123
r_chiral_restr	0.121
r_symmetry_xyhbond_nbd_refined	0.118
r_xyhbond_nbd_refined	0.11
r_symmetry_nbd_refined	0.073
r_symmetry_nbtor_other	0.063
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2417
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	68

Software

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