2OSW | pdb_00002osw

Endo-glycoceramidase II from Rhodococcus sp.

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
2.24	45.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.75	α = 90
b = 92.941	β = 98.55
c = 94.545	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		2005-11-11	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	1.6	30.979	99.2	0.053	0.053	9.5	6.4		119859			19.957

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)
	1.6	1.69	98.2		0.335	0.335	2.2	6.4	17253

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	29.57	119829	6081	99.1	0.183	0.181	0.19	0.204	0.21	RANDOM	13.701

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]
0.93		-0.36	0.22		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.44
r_dihedral_angle_3_deg	11.774
r_dihedral_angle_4_deg	10.171
r_dihedral_angle_1_deg	5.717
r_scangle_it	1.659
r_angle_refined_deg	1.059
r_scbond_it	1.057
r_angle_other_deg	0.846
r_mcangle_it	0.747
r_mcbond_it	0.413
r_symmetry_vdw_other	0.257
r_nbd_refined	0.196
r_nbd_other	0.19
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.135
r_mcbond_other	0.132
r_metal_ion_refined	0.094
r_xyhbond_nbd_refined	0.091
r_symmetry_hbond_refined	0.084
r_nbtor_other	0.082
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6877
Nucleic Acid Atoms
Solvent Atoms	880
Heterogen Atoms	20

Software

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