2IXB

Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.25		46-50% 2-METHYL-2,4-PENTANEDIOL (MPD), 75 MM NA-CITRATE PH 6.25

Crystal Properties
Matthews coefficient	Solvent content
3.44	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.189	α = 90
b = 88.189	β = 90
c = 301.438	γ = 120

Symmetry
Space Group	P 65 2 2

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 CCD		2004-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.4	40	98.2	0.05	33.7	12.3		27626			43.94

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	2.4	2.46	84.3		0.26	9.4	7.8

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 2IXA	2.4	20	26303	1111	97.9	0.174	0.173	0.2	RANDOM	40.62

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]
2.85	1.43		2.85		-4.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.978
r_dihedral_angle_4_deg	18.496
r_dihedral_angle_3_deg	16.313
r_dihedral_angle_1_deg	5.471
r_scangle_it	1.386
r_angle_refined_deg	1.141
r_scbond_it	0.911
r_angle_other_deg	0.85
r_mcangle_it	0.491
r_mcbond_it	0.425
r_symmetry_vdw_other	0.332
r_nbd_other	0.19
r_nbd_refined	0.18
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.135
r_symmetry_vdw_refined	0.134
r_nbtor_other	0.083
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	3402
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling