2EPK | pdb_00002epk

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

X-RAY DIFFRACTION

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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
3.92	68.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.895	α = 90
b = 124.509	β = 90
c = 148.536	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	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97928, 0.97945, 0.94929	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	1.85	39.97	99.64	0.1	13.4	7.4	97867	97524	3	3	26.7

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	1.85	1.9	95.58		0.65	3.24	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.85	39.97	97400	92648	4876	99.64	0.21605	0.21506	0.2	0.2347	0.22	RANDOM	30.89

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]
-2.84			-1.89		4.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.745
r_dihedral_angle_4_deg	15.861
r_dihedral_angle_3_deg	13.351
r_dihedral_angle_1_deg	7.303
r_scangle_it	6.158
r_scbond_it	4.686
r_mcangle_it	2.986
r_mcbond_it	2.525
r_angle_refined_deg	1.224
r_angle_other_deg	0.77
r_mcbond_other	0.626
r_symmetry_vdw_other	0.258
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.21
r_nbtor_refined	0.187
r_nbd_other	0.174
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.126
r_nbtor_other	0.082
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4984
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	35

Software

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