2CBI

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000) AND 0.25 MICROLITER OF 40 % V/V GAMMA-BUTYROLACTONE TO A 1 PLUS MICROLITER DROP

Crystal Properties
Matthews coefficient	Solvent content
2.51	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.939	α = 90
b = 147.38	β = 90
c = 157.687	γ = 90

Symmetry
Space Group	I 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	157	CCD	MARRESEARCH	MIRROR	2005-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.25	20	100	0.11	7.7	25.4		65956		2

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	2.25	2.33	100		0.48	7.6	18.6

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	SAD	THROUGHOUT	2.25	20	65296	659	99.9	0.169	0.169	0.22	RANDOM	14.66

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]
0.92			1.62		-2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.218
r_dihedral_angle_4_deg	20.703
r_dihedral_angle_3_deg	16.27
r_dihedral_angle_1_deg	6.373
r_scangle_it	5.034
r_scbond_it	3.436
r_mcangle_it	1.954
r_angle_refined_deg	1.47
r_mcbond_it	1.266
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9240
Nucleic Acid Atoms
Solvent Atoms	650
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing