9F09

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with 2-deoxyribose, 7-Bromo-1H-imidazo[4,5-b]pyridine and 2'-deoxycytidine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F8Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.2 M sodium citrate; 20% PEG 3350 pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.885	α = 90
b = 148.885	β = 90
c = 148.885	γ = 90

Symmetry
Space Group	I 21 3

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		2024-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976277	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	2.37	60.856	100	0.09	0.02	1	33.3	41.7		22441			56

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	2.37	2.46			1.48	0.32	0.91	3.6	43.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.37	60.856	22439	1133	99.982	0.185	0.184	0.211	59.782

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	19.764
r_dihedral_angle_3_deg	14.849
r_dihedral_angle_6_deg	13.034
r_lrange_it	10.629
r_lrange_other	10.628
r_dihedral_angle_2_deg	9.986
r_scangle_it	8.795
r_scangle_other	8.793
r_mcangle_it	7.317
r_mcangle_other	7.315
r_scbond_it	6.42
r_scbond_other	6.419
r_dihedral_angle_1_deg	6.401
r_mcbond_it	5.514
r_mcbond_other	5.494
r_angle_refined_deg	1.695
r_angle_other_deg	0.605
r_symmetry_xyhbond_nbd_other	0.442
r_xyhbond_nbd_refined	0.243
r_nbd_other	0.241
r_nbd_refined	0.227
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.187
r_symmetry_nbd_refined	0.154
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.087
r_ncsr_local_group_1	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2524
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	44

Software

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