8XSH | pdb_00008xsh

Crystal structure of the Actinobacillus minor NM305 glucosyltransferase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-B3H2N1-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES pH 6.5, 0.2 M sodium formate, 14% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.592	α = 90
b = 44.312	β = 113.745
c = 90.754	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M		2022-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	50	98.9	0.02	0.998	38.7	1.9		29001

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89			0.099	0.885

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	AlphaFold(AF-B3H2N1-F1)	1.85	46.487	29000	1425	98.787	0.159	0.1563	0.1563	0.2111	0.2106	11.551

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]
1.41		0.292	-2.078		0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.081
r_dihedral_angle_3_deg	14.545
r_dihedral_angle_2_deg	9.279
r_dihedral_angle_1_deg	6.481
r_rigid_bond_restr	3.376
r_lrange_it	2.133
r_lrange_other	2.024
r_angle_refined_deg	1.466
r_scangle_it	1.159
r_scangle_other	1.159
r_mcangle_it	1.026
r_mcangle_other	1.026
r_scbond_it	0.845
r_scbond_other	0.845
r_mcbond_it	0.645
r_mcbond_other	0.645
r_angle_other_deg	0.5
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.216
r_nbd_other	0.21
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.022
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2779
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms

Software

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