3AFL

Crystal structure of exotype alginate lyase Atu3025 H531A complexed with alginate trisaccharide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	17% PEG 4000, 8.5% iso-propanol, 0.085M HEPES-Na, 15% glycerol, 10mM alginate trisaccharide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.845	α = 90
b = 99.643	β = 90
c = 109.168	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	100	CCD	ADSC QUANTUM 210		2009-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.000	SPring-8	BL38B1

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	2.99	50	99.5	0.099	11.2	4.2		18590

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	2.99	3.11	99.9		0.361	4.9	4.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3A0O	2.99	37.85	17479	943	99.02	0.20211	0.19888	0.26234	RANDOM	37.671

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]
-3.36			6.5		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.088
r_dihedral_angle_4_deg	18.065
r_dihedral_angle_3_deg	17.305
r_dihedral_angle_1_deg	5.629
r_scangle_it	1.284
r_angle_refined_deg	1.064
r_scbond_it	0.734
r_mcangle_it	0.637
r_mcbond_it	0.347
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.088
r_dihedral_angle_4_deg	18.065
r_dihedral_angle_3_deg	17.305
r_dihedral_angle_1_deg	5.629
r_scangle_it	1.284
r_angle_refined_deg	1.064
r_scbond_it	0.734
r_mcangle_it	0.637
r_mcbond_it	0.347
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.236
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6149
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	36

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.