7YQS | pdb_00007yqs

Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Protein solution : protein 24mg/ml, 20mM Tris-DCl (pD 8.0), Reservoir solution : 33 % (w/v) PEG 1500, 0.1 M Tris-DCl (pD 8.5), 0.1 M L-Rha

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.78	α = 90
b = 65.8	β = 90
c = 108.95	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	293	PIXEL	DECTRIS PILATUS3 S 6M		2021-03-17	M	SINGLE WAVELENGTH
2	1	neutron	293	DIFFRACTOMETER	iBIX		2021-02-12	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.28-6.19	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.25	43.42	100	0.059			0.025	0.999		15	6.4		115388			14.58
2	1.8	19.82	98.9	0.257			0.096	0.983		8.4	7.9		38826		-3	14.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27		0.886			0.38	0.794		2.2	6.4
2	1.8	1.86		1.174			0.507	0.411		1.6	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	1.25	43.42		1.33		115291	5764	99.96		0.1474	0.1465	0.15	0.163	0.16		33.31
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.8	19.82				38824	1946	99		0.1634	0.1619		0.1907

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.2464
f_angle_d	1.1603
f_chiral_restr	0.0911
f_bond_d	0.0071
f_plane_restr	0.0058

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3337
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	108

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement

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.