3D52 | pdb_00003d52

GOLGI MANNOSIDASE II complex with an N-aryl carbamate derivative of gluco-hydroxyiminolactam

X-RAY DIFFRACTION

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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
2.12	41.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.579	α = 90
b = 107.912	β = 90
c = 137.062	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	0.977	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	1.6	20	97.4	0.087	13.7	4.99	134545	131084

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)
	1.6	1.63	96.9		0.208	7.37	5.3	4837

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	19.72	134349	131030	1940	97.53	0.229	0.228	0.2086	0.24	0.2079	RANDOM	17.147

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			-0.04		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.342
r_dihedral_angle_4_deg	18.707
r_dihedral_angle_3_deg	12.833
r_dihedral_angle_1_deg	6.352
r_scangle_it	4.384
r_scbond_it	2.908
r_mcangle_it	1.948
r_angle_refined_deg	1.863
r_mcbond_it	1.363
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.199
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.119
r_bond_refined_d	0.017
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8209
Nucleic Acid Atoms
Solvent Atoms	875
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