3CMG | pdb_00003cmg

Crystal structure of putative beta-galactosidase from Bacteroides fragilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.1M Tris-HCl pH 8.5, 50% MPD, 0.22M Ammonium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.651	α = 90
b = 102.878	β = 90
c = 199.967	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	ADSC QUANTUM 315		2008-03-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-03-05	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X6A	0.979	NSLS	X6A

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	1.9	50	99.5	0.088	0.065	5.6	5.1	124005	124005

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	1.9	1.97	96.3		0.423	0.337	2.4	4.3	11983

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	39.84	64465	64465	3256	99.5	0.15	0.15	0.148	0.1493	0.186	RANDOM	24.874

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]
3.38			-0.96		-2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	20.623
r_dihedral_angle_3_deg	12.576
r_dihedral_angle_1_deg	6.44
r_scangle_it	4.367
r_mcangle_it	3.418
r_scbond_it	3.056
r_mcbond_it	2.516
r_angle_refined_deg	1.376
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.207
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5357
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXE	model building
SHELXD	phasing