2EPM | pdb_00002epm

N-acetyl-B-D-glucoasminidase (GCNA) from Stretococcus gordonii

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	293	100mM Tris, 1.9M ammonium sulphate, 0.5%(v/v) PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.964	α = 90
b = 124.746	β = 90
c = 147.889	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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirrors	2006-12-12	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	2.04	14.95	99.31	0.064	18.9	8.1	72240	71742	3	3	26.6

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	2.04	2.09	94.31		0.35	3.74	7.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2EPL	2.04	14.95	72240	68128	3614	99.31	0.20091	0.20091	0.199	0.19	0.23699	0.22	RANDOM	40.635

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]
-2.4			-1.41		3.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.656
r_dihedral_angle_4_deg	16.318
r_dihedral_angle_3_deg	12.946
r_scangle_it	6.591
r_dihedral_angle_1_deg	5.871
r_scbond_it	5.048
r_mcangle_it	3.145
r_mcbond_it	2.772
r_angle_refined_deg	1.245
r_angle_other_deg	0.764
r_mcbond_other	0.68
r_symmetry_vdw_refined	0.234
r_symmetry_vdw_other	0.233
r_nbd_refined	0.213
r_nbtor_refined	0.188
r_nbd_other	0.174
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.135
r_nbtor_other	0.083
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4798
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	47

Software

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