3BUB

Golgi alpha-mannosidase II with an empty active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.765	α = 90
b = 109.624	β = 90
c = 138.649	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		2007-04-20	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	20	98.5	0.06	20.7	6.4	214738	211715			18

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		0.33	3.5	2.3	3723

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	19.81	214738	210432	3138	97.99	0.18	0.18	0.204	RANDOM	14.616

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.699
r_dihedral_angle_4_deg	18.041
r_dihedral_angle_3_deg	12.552
r_dihedral_angle_1_deg	6.08
r_scangle_it	3.72
r_scbond_it	2.411
r_mcangle_it	1.68
r_angle_refined_deg	1.544
r_mcbond_it	1.044
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.103
r_metal_ion_refined	0.038
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8196
Nucleic Acid Atoms
Solvent Atoms	1470
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SADABS	data scaling
CNS	phasing