6UFL

Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei (AmGH128_I) in the complex with laminarihexaose

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20% (w/v) Polyethylene glycol 3.350, 0.2 M Potassium Thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.096	α = 90
b = 77.757	β = 101.99
c = 46.481	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	IMAGE PLATE	RIGAKU RAXIS IV		2019-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.61	50	94	0.995	9.3	3		32212

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	1.61	1.71	90		0.835	1.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.61	45.47	32211	1611	94	0.187	0.2	0.227	0.23	20.57

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]
0.53		1.319	-0.515		-0.528

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.315
r_dihedral_angle_4_deg	13.656
r_dihedral_angle_3_deg	11.975
r_dihedral_angle_1_deg	7.208
r_angle_other_deg	3.211
r_scangle_other	2.783
r_scangle_it	2.718
r_mcangle_it	2.163
r_mcangle_other	2.135
r_angle_refined_deg	2.063
r_scbond_it	1.845
r_scbond_other	1.844
r_mcbond_it	1.444
r_mcbond_other	1.359
r_nbd_other	0.24
r_nbd_refined	0.206
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.11
r_bond_other_d	0.036
r_gen_planes_other	0.033
r_gen_planes_refined	0.016
r_bond_refined_d	0.015
r_nbtor_other
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_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1813
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing