9RDD | pdb_00009rdd

Nicotinic Acid N-glucoside Reductase NaGR (A622) in complex with NADP+ and Nicotinic Acid N-glucoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	P52579

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.1M HEPES pH 7.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.586	α = 73.2
b = 45.531	β = 79.99
c = 53.473	γ = 69.64

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	120	PIXEL	DECTRIS EIGER2 XE 16M		2024-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.70542	Diamond	I03

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	1.278	51.02	87	0.07	0.049	0.996	8	3.8		44163

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	1.278	1.544			0.614	0.614	0.592	1.6	3.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.28	51.02	42211	2236	51.38	0.17114	0.1691	0.1692	0.21013	0.2103	RANDOM	17.396

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]
	-0.06	-0.02	0.02	0.03	-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.666
r_dihedral_angle_2_deg	10.807
r_dihedral_angle_1_deg	6.415
r_long_range_B_refined	5.926
r_long_range_B_other	5.69
r_scangle_other	4.069
r_mcangle_other	3.039
r_mcangle_it	3.038
r_scbond_it	2.572
r_scbond_other	2.571
r_mcbond_it	1.965
r_mcbond_other	1.965
r_angle_refined_deg	1.88
r_angle_other_deg	0.616
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2406
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing