2EPL

N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		accompanying SeMet structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.1	293	100mM Tris, 2M ammonium sulphate, 2 %(v/v) PEG400, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.561	α = 90
b = 124.535	β = 90
c = 147.793	γ = 90

Symmetry
Space Group	I 2 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	MARRESEARCH		2006-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97928	APS	23-ID-D

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	1.4	29.4	99.88	0.09	17.8	9.8	222135	221868	3	3	18.5

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	1.4	1.44	99.39		0.5	2.53	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	accompanying SeMet structure	1.4	29.39	221868	210780	11088	99.88	0.18699	0.18699	0.18635	0.19905	RANDOM	20.709

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]
-1.8			-1.09		2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_4_deg	16.711
r_dihedral_angle_3_deg	11.834
r_dihedral_angle_1_deg	5.79
r_scangle_it	5.594
r_scbond_it	4.052
r_mcangle_it	2.574
r_mcbond_it	2.338
r_angle_refined_deg	1.304
r_angle_other_deg	0.814
r_mcbond_other	0.492
r_symmetry_vdw_other	0.251
r_symmetry_vdw_refined	0.244
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.212
r_nbtor_refined	0.185
r_nbd_other	0.174
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.08
r_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4992
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling