5L77

A glycoside hydrolase mutant with an unreacted activity based probe bound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	12 mg/mL protein stock in mixed 1:1 with 1.2 M NaH2PO4/K2HPO4 (1:9 v/v) at 293 K.

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.17	α = 90
b = 45.12	β = 115.11
c = 82.04	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS3 6M		2015-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.24	28.88	89.8	0.998	13.7	3.9		126454

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	3VYO	1.24	28.88	120177	6276	89.59	0.13084	0.12933	0.16028	RANDOM	18.698

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]
0.28		1.26	-1.49		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.355
r_sphericity_free	32.156
r_sphericity_bonded	13.297
r_dihedral_angle_3_deg	11.838
r_dihedral_angle_4_deg	11.594
r_dihedral_angle_1_deg	5.798
r_long_range_B_refined	4.344
r_long_range_B_other	4.344
r_scangle_other	3.397
r_scbond_it	2.837
r_scbond_other	2.834
r_rigid_bond_restr	2.685
r_mcangle_other	2.43
r_mcangle_it	2.429
r_mcbond_it	1.953
r_mcbond_other	1.953
r_angle_refined_deg	1.734
r_angle_other_deg	1.059
r_chiral_restr	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3457
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing