6JP4

Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	298	15% PEG 6000, 0.1 M magnesium acetate

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 261.324	α = 90
b = 394.812	β = 90
c = 112.187	γ = 90

Symmetry
Space Group	C 2 2 21

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 1		2018-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97179	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.069	98.898	99.5	0.992	11	7.3		348350			32.327

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.069	2.11			0.541	1.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.069	98.898	348322	17175	99.458	0.223	0.2221	0.2402	45.922

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]
-1.517			-0.122		1.639

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.892
r_dihedral_angle_4_deg	16.26
r_dihedral_angle_3_deg	13.36
r_lrange_it	7.91
r_lrange_other	7.91
r_dihedral_angle_1_deg	7.19
r_scangle_it	6.481
r_scangle_other	6.481
r_scbond_it	5.19
r_scbond_other	5.19
r_mcangle_it	4.677
r_mcangle_other	4.677
r_mcbond_it	3.557
r_mcbond_other	3.557
r_angle_refined_deg	1.515
r_angle_other_deg	1.387
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_other	0.232
r_nbd_refined	0.195
r_metal_ion_refined	0.187
r_symmetry_nbd_other	0.181
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_other	0.153
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.074
r_ncsr_local_group_1	0.043
r_ncsr_local_group_2	0.04
r_ncsr_local_group_3	0.04
r_ncsr_local_group_4	0.04
r_ncsr_local_group_5	0.039
r_ncsr_local_group_6	0.038
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21800
Nucleic Acid Atoms
Solvent Atoms	832
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
pointless	data scaling
SHELX	phasing