3BVV | pdb_00003bvv

Golgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-D-MANNOPYRANOSIDE

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	293	TRIS, NACL, PEG6000, MPD. Crystals washed in phosphate buffered reservoir solution before soaking with substrate for 24 hrs, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.104	α = 90
b = 109.815	β = 90
c = 139.303	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		2005-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.972	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	1.3	20	97.8	0.08	17.2	7.6	260486	254755

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)
	1.3	1.32	78.4		0.26	4.8	3.6

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	PDB entry 1HTY	1.3	19.61	260346	254592	3796	97.79	0.153	0.152	0.15	0.173	0.15	RANDOM	16.368

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	36.988
r_dihedral_angle_4_deg	17.691
r_dihedral_angle_3_deg	12.439
r_dihedral_angle_1_deg	6.201
r_sphericity_free	4.005
r_scangle_it	3.45
r_sphericity_bonded	3.401
r_scbond_it	2.43
r_mcangle_it	1.799
r_angle_refined_deg	1.461
r_rigid_bond_restr	1.447
r_mcbond_it	1.257
r_nbtor_refined	0.309
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_metal_ion_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8581
Nucleic Acid Atoms
Solvent Atoms	1706
Heterogen Atoms	49

Software

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