6RS0

GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3S,4R,5R)-1-(2-(Benzyloxy)ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.984	α = 90
b = 91.437	β = 90
c = 132.46	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		2019-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	75.25	99.5	0.997	12.4	8.2		100041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	98.8		0.737	1.2	8.4

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3BUB	1.8	75.25	94987	4975	99.33	0.1955	0.1933	0.2369	RANDOM	35.909

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]
-2.47			3.48		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.232
r_dihedral_angle_4_deg	19.039
r_dihedral_angle_3_deg	14.868
r_dihedral_angle_1_deg	7.471
r_mcangle_it	4.005
r_mcbond_it	2.88
r_mcbond_other	2.88
r_angle_other_deg	2.326
r_angle_refined_deg	1.524
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.232
r_dihedral_angle_4_deg	19.039
r_dihedral_angle_3_deg	14.868
r_dihedral_angle_1_deg	7.471
r_mcangle_it	4.005
r_mcbond_it	2.88
r_mcbond_other	2.88
r_angle_other_deg	2.326
r_angle_refined_deg	1.524
r_chiral_restr	0.075
r_bond_other_d	0.035
r_gen_planes_other	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8057
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

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 R01GM133198.