3DX4

Golgi alpha-Mannosidase II in complex with Mannostatin analog (1R,2R,3R,4S,5R)-4-amino-5-methoxycyclopentane-1,2,3-triol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HTY	PDB entry 1HTY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.769	α = 90
b = 109.703	β = 90
c = 138.306	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	CCD	ADSC QUANTUM 4		2007-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9770	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.38	40	99.6	0.078	24.2	14.6		212071

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.4	82.8		0.41	5.2	6.7	2887

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 1HTY	1.38	19.5	212538	211539	3136	99.53	0.188	0.188	0.203	RANDOM	15.957

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.492
r_dihedral_angle_4_deg	17.371
r_dihedral_angle_3_deg	11.731
r_dihedral_angle_1_deg	6.075
r_scangle_it	3.554
r_scbond_it	2.337
r_mcangle_it	1.632
r_angle_refined_deg	1.593
r_mcbond_it	1.07
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.492
r_dihedral_angle_4_deg	17.371
r_dihedral_angle_3_deg	11.731
r_dihedral_angle_1_deg	6.075
r_scangle_it	3.554
r_scbond_it	2.337
r_mcangle_it	1.632
r_angle_refined_deg	1.593
r_mcbond_it	1.07
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.231
r_chiral_restr	0.157
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.137
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8197
Nucleic Acid Atoms
Solvent Atoms	1304
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SADABS	data scaling
CNS	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.