2OYM

Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSW	PDB ENTRY 2OSW

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
2.25	45.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.786	α = 90
b = 93.282	β = 98.3
c = 94.471	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MAR scanner 345 mm plate		2006-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.841	18.3	91.9	0.048	0.048	14.1	4		72622			21.22

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)
	1.841	1.95	75.4		0.346	0.346	2.2	3.9	8650

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2OSW	1.86	18.3	72620	3701	93.43	0.182	0.18	0.212	RANDOM	16.128

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]
1.09		-0.16	0.46		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.677
r_dihedral_angle_3_deg	12.039
r_dihedral_angle_4_deg	9.876
r_dihedral_angle_1_deg	5.98
r_scangle_it	1.92
r_scbond_it	1.219
r_angle_refined_deg	1.196
r_angle_other_deg	0.894
r_mcangle_it	0.88
r_mcbond_it	0.492
r_nbd_other	0.192
r_nbd_refined	0.191
r_nbtor_refined	0.176
r_symmetry_vdw_other	0.149
r_mcbond_other	0.147
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.125
r_symmetry_vdw_refined	0.109
r_metal_ion_refined	0.092
r_nbtor_other	0.083
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6773
Nucleic Acid Atoms
Solvent Atoms	675
Heterogen Atoms	46

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling