3ECQ | pdb_00003ecq

Endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae: SeMet structure

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	29% (w/v) PEG MME 2000, 0.2 M lithium citrate, 0.1 M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.611	α = 90
b = 158.209	β = 90
c = 112.436	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	CCD	ADSC QUANTUM 315		2006-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9795	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.9	112.509	99.4	0.11	0.11	6.13	6.8		83445			71.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	97.4		0.592	0.592	2.4	6.3	11781

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2.9	112.509	83381	4164	99.37	0.192	0.19	0.1977	0.235	0.2394	RANDOM	57.319

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]
-0.99			0.91		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.55
r_dihedral_angle_4_deg	18.645
r_dihedral_angle_3_deg	16.777
r_dihedral_angle_1_deg	6.587
r_scangle_it	2.069
r_scbond_it	1.313
r_angle_refined_deg	1.225
r_angle_other_deg	0.823
r_mcangle_it	0.625
r_symmetry_hbond_refined	0.331
r_mcbond_it	0.286
r_nbd_refined	0.207
r_nbd_other	0.189
r_metal_ion_refined	0.187
r_nbtor_refined	0.186
r_symmetry_vdw_other	0.168
r_xyhbond_nbd_refined	0.136
r_symmetry_vdw_refined	0.125
r_nbtor_other	0.086
r_mcbond_other	0.08
r_chiral_restr	0.071
r_xyhbond_nbd_other	0.022
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21250
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction