4XWH

Crystal structure of the human N-acetyl-alpha-glucosaminidase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	1.0 M lithium sulfate, 0.01 M nickel chloride, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
5.94	79.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.088	α = 90
b = 205.088	β = 90
c = 78.398	γ = 120

Symmetry
Space Group	P 63

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		2010-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

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	2.32	100	100	0.086	20.7	9.5		81740			45.2

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	2.32	2.4	99.8		0.763	1.85	5.8

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	2VCC	2.32	100	77480	3993	99.56	0.1669	0.16591	0.18579	RANDOM	53.533

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]
0.07	0.04		0.07		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.31
r_dihedral_angle_4_deg	19.703
r_dihedral_angle_3_deg	18.275
r_dihedral_angle_1_deg	6.162
r_long_range_B_refined	5.717
r_long_range_B_other	5.695
r_scangle_other	3.779
r_scbond_it	2.375
r_scbond_other	2.374
r_mcangle_it	2.239
r_mcangle_other	2.239
r_angle_refined_deg	1.776
r_mcbond_other	1.461
r_mcbond_it	1.46
r_angle_other_deg	1.11
r_chiral_restr	0.127
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5693
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	175

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction