6RRY

GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol

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
2.34	47.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.473	α = 90
b = 90.366	β = 90
c = 132.772	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		2019-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.950	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	1.86	90.37	100	0.996	12.4	8.1		91011

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	1.86	1.89	100		0.705	1.3

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	1.86	74.31	86399	4527	99.95	0.1881	0.1859	0.2328	RANDOM	34.862

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			2.32		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.554
r_dihedral_angle_4_deg	17.635
r_dihedral_angle_3_deg	13.98
r_dihedral_angle_1_deg	7.413
r_mcangle_it	3.85
r_mcbond_it	2.814
r_mcbond_other	2.812
r_angle_other_deg	2.347
r_angle_refined_deg	1.543
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.554
r_dihedral_angle_4_deg	17.635
r_dihedral_angle_3_deg	13.98
r_dihedral_angle_1_deg	7.413
r_mcangle_it	3.85
r_mcbond_it	2.814
r_mcbond_other	2.812
r_angle_other_deg	2.347
r_angle_refined_deg	1.543
r_chiral_restr	0.076
r_bond_other_d	0.035
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8065
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	30

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.