3EJP | pdb_00003ejp

Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog: (5R)-5-[2'-oxo-2'-(phenyl)ethyl]-swainsonine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BUB

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.025	α = 90
b = 109.883	β = 90
c = 138.959	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		2004-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9186	CHESS	F1

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	1.32	30	97.7	0.072	15.3	5.04	247309	241556

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	1.32	1.34	87.5		0.276	4.46	3.21	5479

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3BUB	1.32	29.22	247145	227621	5203	92.1	0.157	0.157	0.16	0.182	0.15	RANDOM	15.273

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			0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.659
r_dihedral_angle_4_deg	19.187
r_dihedral_angle_3_deg	12.083
r_dihedral_angle_1_deg	6.049
r_sphericity_free	5.058
r_sphericity_bonded	3.721
r_scangle_it	3.393
r_scbond_it	2.526
r_mcangle_it	1.793
r_rigid_bond_restr	1.747
r_angle_refined_deg	1.395
r_mcbond_it	1.235
r_nbtor_refined	0.308
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.125
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8193
Nucleic Acid Atoms
Solvent Atoms	1295
Heterogen Atoms	44

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