2OW7 | pdb_00002ow7

Golgi alpha-mannosidase II complex with (1R,6S,7R,8S)-1-thioniabicyclo[4.3.0]nonan-7,8-diol chloride

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	Tris, PEG 6K, MPD, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 108.58	β = 90
c = 137.779	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	BRUKER SMART 6000		2007-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	1.77	20	99.5	0.0606	19.8	7.21	101363	100893	1	1

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	1.77	1.81	92.9		0.402	3.14	3.2

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	1hty	1.77	10.54	101010	100293	1509	99.59	0.162	0.162	0.17	0.203	0.17	RANDOM	16.853

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	38.098
r_dihedral_angle_4_deg	18.318
r_dihedral_angle_3_deg	13.972
r_dihedral_angle_1_deg	6.941
r_scangle_it	4.758
r_scbond_it	3.204
r_angle_refined_deg	2.023
r_mcangle_it	1.993
r_mcbond_it	1.365
r_symmetry_vdw_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.098
r_dihedral_angle_4_deg	18.318
r_dihedral_angle_3_deg	13.972
r_dihedral_angle_1_deg	6.941
r_scangle_it	4.758
r_scbond_it	3.204
r_angle_refined_deg	2.023
r_mcangle_it	1.993
r_mcbond_it	1.365
r_symmetry_vdw_refined	0.328
r_nbtor_refined	0.309
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.207
r_chiral_restr	0.159
r_symmetry_hbond_refined	0.149
r_bond_refined_d	0.026
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8190
Nucleic Acid Atoms
Solvent Atoms	1115
Heterogen Atoms	59

Software

Software
Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	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.