5AXG | pdb_00005axg

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WNK	Bacillus circulans T-3040 CITase (3WNK)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10	293	1.35 M sodium dihydrogenphosphate dihydrate, 0.9 M potassium phosphate dibasic, 0.2 M lithium sulfate, 0.1 M 3-(cyclohexylamino)propane-1-sulfonic acid (pH 10.5)

Crystal Properties
Matthews coefficient	Solvent content
2.42	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.342	α = 90
b = 98.992	β = 90
c = 171.13	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2012-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	85.69	100	0.076	28.5	8.6		118811		-3

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	1.88	100		0.606	3.8	8.6

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	Bacillus circulans T-3040 CITase (3WNK)	1.85	85.69	112028	5907	99.62	0.167	0.16575	0.18	0.19046	0.2	RANDOM	23.489

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]
0.31			-0.27		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.697
r_dihedral_angle_4_deg	15.28
r_dihedral_angle_3_deg	12.474
r_dihedral_angle_1_deg	6.171
r_long_range_B_refined	4.99
r_long_range_B_other	4.913
r_scangle_other	2.348
r_mcangle_it	1.916
r_mcangle_other	1.916
r_scbond_it	1.405
r_scbond_other	1.405
r_angle_refined_deg	1.215
r_mcbond_it	1.118
r_mcbond_other	1.118
r_angle_other_deg	0.895
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9522
Nucleic Acid Atoms
Solvent Atoms	889
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing