7FHU | pdb_00007fhu

Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 8.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QAZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298.15	0.2M lithium sulfate monohydrate, 0.1M Tris-HCl pH-8.5, 30% (w/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.17	42.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.022	α = 90
b = 66.804	β = 94.386
c = 103.12	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	CMOS	BRUKER PHOTON 100	HELIOS-MX	2016-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.5418

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	2.43	43.89	100	0.1232	0.998	19.97	17.66		22678

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	2.43	2.53	100		0.4421	0.948	5.11	11.4

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	1QAZ	2.43	43.854	22476	1033	99.153	0.229	0.2273	0.23	0.2737	0.27	21.892

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]
1.836		-0.475	-1.864		0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.583
r_dihedral_angle_4_deg	20.319
r_dihedral_angle_3_deg	14.168
r_dihedral_angle_1_deg	5.532
r_lrange_it	4.589
r_lrange_other	4.546
r_scangle_it	3.403
r_scangle_other	3.396
r_scbond_it	2.88
r_scbond_other	2.877
r_mcangle_it	2.643
r_mcangle_other	2.643
r_mcbond_it	1.659
r_mcbond_other	1.659
r_angle_other_deg	1.429
r_angle_refined_deg	1.227
r_nbd_other	0.23
r_symmetry_nbd_other	0.198
r_nbd_refined	0.194
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.075
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4782
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	25

Software

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