9FTR | pdb_00009ftr

Drosophila golgi alpha-mannosidase II (dGMII) in complex with amide modified swainsonine-configured alkyl indolizidine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM succinate pH 7.0 and 6-12% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.113	α = 90
b = 91.939	β = 90
c = 133.241	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 EIGER X 16M		2023-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.14	57.681	100	0.045	0.045	0.997	9.6	1.9		61056

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	2.14	2.2	100		0.352	0.352	0.682	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	NONE	2.14	57.681	61056	1578	99.989	0.181	0.1794	0.1793	0.2589	0.2591	37.487

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]
-1.64			0.729		0.911

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.391
r_dihedral_angle_6_deg	15.212
r_dihedral_angle_2_deg	10.114
r_lrange_it	8.926
r_dihedral_angle_1_deg	8.349
r_scangle_it	8.048
r_mcangle_it	6.4
r_scbond_it	6.308
r_mcbond_it	5.062
r_angle_refined_deg	2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.391
r_dihedral_angle_6_deg	15.212
r_dihedral_angle_2_deg	10.114
r_lrange_it	8.926
r_dihedral_angle_1_deg	8.349
r_scangle_it	8.048
r_mcangle_it	6.4
r_scbond_it	6.308
r_mcbond_it	5.062
r_angle_refined_deg	2.58
r_symmetry_xyhbond_nbd_refined	0.68
r_symmetry_nbd_refined	0.517
r_nbtor_refined	0.298
r_nbd_refined	0.196
r_chiral_restr	0.183
r_xyhbond_nbd_refined	0.134
r_bond_refined_d	0.014
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7902
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	107

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.