5FKR

Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LGN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M TRIS (PH 7.8), 0.3 M POTASSIUM BROMIDE, 8 % PGA-LM

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.89	α = 90
b = 131.91	β = 90
c = 73.17	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS 6M-F		2014-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.28	73.17	99.8	0.13	11.4	6.5		39506		2

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	2.28	2.34	99.6		0.62	2.8	6.6

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	4LGN	2.28	73.17	37512	1948	99.77	0.21265	0.20969	0.26836	RANDOM	28.639

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]
-1.89			6.14		-4.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.785
r_dihedral_angle_4_deg	16.65
r_dihedral_angle_3_deg	13.813
r_dihedral_angle_1_deg	7.594
r_long_range_B_refined	4.294
r_long_range_B_other	4.265
r_mcangle_it	2.805
r_mcangle_other	2.805
r_scangle_other	2.75
r_mcbond_it	1.84
r_mcbond_other	1.84
r_scbond_it	1.804
r_scbond_other	1.804
r_angle_refined_deg	1.658
r_angle_other_deg	1.023
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5538
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing