2OSX

Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.801	α = 90
b = 61.984	β = 112.25
c = 102.846	γ = 90

Symmetry
Space Group	C 1 2 1

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 315		2006-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.1	31.734	93.8	0.054	0.054	9.2	4.2		171712			7.094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	89.9		0.463	0.463	1.5	4.2	23927

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.1	46.23	171710	8690	93.86	0.122	0.121	0.139	RANDOM	7.65

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]
0.08		0.03	-0.19		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.712
r_dihedral_angle_4_deg	12.93
r_dihedral_angle_3_deg	11.374
r_sphericity_free	6.678
r_dihedral_angle_1_deg	6.178
r_sphericity_bonded	3.68
r_scangle_it	2.942
r_scbond_it	2.206
r_mcangle_it	1.742
r_angle_refined_deg	1.468
r_mcbond_it	1.159
r_rigid_bond_restr	0.975
r_angle_other_deg	0.955
r_mcbond_other	0.596
r_symmetry_vdw_refined	0.348
r_symmetry_vdw_other	0.292
r_nbd_refined	0.212
r_nbd_other	0.207
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.131
r_metal_ion_refined	0.13
r_chiral_restr	0.09
r_nbtor_other	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3452
Nucleic Acid Atoms
Solvent Atoms	598
Heterogen Atoms	73

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing