1W2T | pdb_00001w2t

beta-fructosidase from Thermotoga maritima in complex with raffinose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UYP	PDB ENTRY 1UYP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	HANGING DROP TECHNIQUE 10% PEG 1000, 50 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2, CONCENTRATION PROTEIN 8 MG/ML, INCUBATION TEMPERATURE 20 C

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.5	α = 90
b = 114.7	β = 98.9
c = 130	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	294	CCD	ADSC CCD	MIRRORS	2004-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.87	129.099	97.7	0.062	6	3.3		225700

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	1.87	30	97.8		0.184	3.9	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UYP	1.87	40	209387	11055	97.7	0.199	0.198	0.21	0.229	0.24	RANDOM	15.8

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]
0.91		1.14	-0.64		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.484
r_scangle_it	1.729
r_angle_refined_deg	1.103
r_scbond_it	1.044
r_angle_other_deg	0.854
r_mcangle_it	0.792
r_symmetry_hbond_refined	0.5
r_mcbond_it	0.413
r_symmetry_vdw_refined	0.293
r_nbd_other	0.233
r_symmetry_vdw_other	0.222
r_nbd_refined	0.183
r_xyhbond_nbd_refined	0.136
r_nbtor_other	0.085
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21109
Nucleic Acid Atoms
Solvent Atoms	1888
Heterogen Atoms	237

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling