9F08 | pdb_00009f08

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Covalent complex with 2-deoxyribose.

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	35% tascimate

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.461	α = 90
b = 148.461	β = 90
c = 148.461	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	60.61	100	0.06	0.01	1	42.5	41.2		22224

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			0.96	0.22	0.95	5.1

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	2.371	60.61	22212	1115	99.982	0.201	0.199	0.2043	0.2284	0.2327	63.329

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_3_deg	16.146
r_dihedral_angle_6_deg	13.764
r_dihedral_angle_2_deg	9.856
r_lrange_other	9.613
r_lrange_it	9.61
r_scangle_it	8.36
r_scangle_other	8.358
r_mcangle_it	7.331
r_mcangle_other	7.329
r_dihedral_angle_1_deg	6.67
r_scbond_it	6.247
r_scbond_other	6.245
r_mcbond_it	5.788
r_mcbond_other	5.783
r_angle_refined_deg	1.661
r_angle_other_deg	0.578
r_nbd_other	0.252
r_nbd_refined	0.22
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbd_refined	0.114
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.091
r_ncsr_local_group_1	0.075
r_bond_refined_d	0.007
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	2523
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	16

Software

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