8QC5

crystal structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ cofactor and citrate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	protein was incubated with 2m M NAD+. crystals were grown in wells containing 1.8 M triammonium citrate pH7

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.863	α = 90
b = 72.817	β = 90
c = 197.307	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 EIGER2 XE 16M		2023-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	49.33	100	0.173	0.18	0.048	0.998	11.9	13.7		60807

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2		100	1.251	1.298	0.343	0.911		14.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	49.3	57694	3029	99.98	0.2001	0.19805	0.23857	RANDOM	29.385

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]
6.34			-3.99		-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.367
r_dihedral_angle_2_deg	15.251
r_dihedral_angle_1_deg	7.813
r_long_range_B_refined	6.064
r_long_range_B_other	6.064
r_scangle_other	4.55
r_mcangle_it	3.258
r_mcangle_other	3.258
r_scbond_it	3.227
r_scbond_other	3.224
r_mcbond_it	2.34
r_mcbond_other	2.339
r_angle_refined_deg	1.336
r_angle_other_deg	0.455
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
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	5533
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing