7FI0 | pdb_00007fi0

Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in ManA bound form at pH-5.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7FHU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298.15	0.2M LiSo4 Monohydrate, 0.1M Sodium acetate pH-5.0, 30% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.757	α = 90
b = 160.662	β = 90
c = 48.16	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	CMOS	BRUKER PHOTON 100		2018-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.31	29.45	95.8	0.155	0.989	10.04	6.39		17710

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.41	80.9		0.5597	0.578	2.14	2.88

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7FHU	2.31	29.402	17692	892	95.726	0.207	0.2049	0.21	0.2515	0.25	20.624

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]
0.726			-1.397		0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.332
r_dihedral_angle_4_deg	21.311
r_dihedral_angle_3_deg	15.484
r_dihedral_angle_1_deg	5.45
r_lrange_it	4.294
r_lrange_other	4.226
r_scangle_it	2.951
r_scangle_other	2.93
r_angle_other_deg	2.668
r_mcangle_it	2.197
r_mcangle_other	2.196
r_scbond_it	1.792
r_scbond_other	1.77
r_angle_refined_deg	1.604
r_mcbond_it	1.362
r_mcbond_other	1.361
r_nbd_other	0.24
r_symmetry_nbd_other	0.222
r_nbd_refined	0.206
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.098
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.035
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2418
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing