9FTQ | pdb_00009ftq

Drosophila golgi alpha-mannosidase II (dGMII) in complex with 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
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.911	α = 90
b = 90.908	β = 90
c = 132.596	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		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.47	74.98	99.9	0.037	0.037	0.998	8	1.9		39207

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.47	2.57			0.215	0.215	0.94	0.9

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	2.47	74.978	39206	1055	99.868	0.21	0.2079	0.2079	0.2977	0.298	52.146

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]
-0.299			0.213		0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_6_deg	13.324
r_lrange_it	10.65
r_dihedral_angle_1_deg	8.389
r_dihedral_angle_2_deg	8.378
r_scangle_it	7.461
r_mcangle_it	7.099
r_scbond_it	4.808
r_mcbond_it	4.543
r_angle_refined_deg	2.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_6_deg	13.324
r_lrange_it	10.65
r_dihedral_angle_1_deg	8.389
r_dihedral_angle_2_deg	8.378
r_scangle_it	7.461
r_mcangle_it	7.099
r_scbond_it	4.808
r_mcbond_it	4.543
r_angle_refined_deg	2.072
r_nbtor_refined	0.278
r_symmetry_nbd_refined	0.179
r_nbd_refined	0.172
r_chiral_restr	0.157
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.133
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7970
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	27

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.