2EPN

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	PDB	2EPK	PDB entry 2EPK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100mM HEPES, 2M ammonium sulphate, 0.5%(v/v) PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.574	α = 90
b = 112.332	β = 90
c = 103.127	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MAR scanner 345 mm plate	mirror	2006-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.61	15.02	99.34	0.064	20.9	9.1	162103	161033	3	3	18.2

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	1.61	1.65	94.37		0.5	3.51	8.4

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	PDB entry 2EPK	1.61	15.02	162103	161033	8028	99.34	0.16912	0.16912	0.1674	0.20186	RANDOM	19.952

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]
1.03			-0.23		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.804
r_dihedral_angle_4_deg	16.349
r_dihedral_angle_3_deg	12.09
r_dihedral_angle_1_deg	5.853
r_scangle_it	5.594
r_scbond_it	4.056
r_mcangle_it	2.577
r_mcbond_it	2.347
r_angle_refined_deg	1.33
r_angle_other_deg	0.805
r_mcbond_other	0.586
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.194
r_nbtor_refined	0.185
r_nbd_other	0.178
r_symmetry_vdw_other	0.172
r_symmetry_hbond_refined	0.112
r_xyhbond_nbd_refined	0.105
r_nbtor_other	0.082
r_chiral_restr	0.081
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	10132
Nucleic Acid Atoms
Solvent Atoms	777
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling