7O84 | pdb_00007o84

Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in complex with substrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		native Pedsa0632

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.2 M Amm chloride, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.182	α = 90
b = 47.583	β = 98.25
c = 116.2	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	100	PIXEL	DECTRIS PILATUS 6M		2017-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.07227	ESRF	ID29

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	2.17	47.58	97.8	0.99	4.8	3.3		46036

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	2.17	2.31			0.43

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	FOURIER SYNTHESIS	THROUGHOUT	native Pedsa0632	2.177	43.97	45831	2282	98.3	0.2312	0.2284	0.24	0.2862	0.3	RANDOM	40.9879

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]
1.0576		-1.9927	-8.1966		7.139

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.71
t_omega_torsion	3.49
t_angle_deg	1.1
t_bond_d	0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.71
t_omega_torsion	3.49
t_angle_deg	1.1
t_bond_d	0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6293
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	84

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.