6Z3I

Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TJK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.139	α = 90
b = 76.67	β = 102.053
c = 67.988	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	PIXEL	DECTRIS EIGER2 XE 16M		2019-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979507	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.8	76.67	100	0.207	0.084	0.995	6.7	7		49541

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	100		2.351	1.301	0.506	0.8	6.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TJK	1.8	66.578	49519	2509	99.962	0.179	0.1782	0.1894	25.448

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]
1.832		1.153	0.507		-2.595

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.291
r_dihedral_angle_4_deg	19.941
r_dihedral_angle_3_deg	13.025
r_dihedral_angle_1_deg	7.487
r_lrange_it	3.832
r_lrange_other	3.666
r_scangle_it	2.355
r_scangle_other	2.355
r_mcangle_it	1.634
r_mcangle_other	1.634
r_scbond_it	1.523
r_scbond_other	1.523
r_angle_refined_deg	1.388
r_angle_other_deg	1.25
r_mcbond_it	1.072
r_mcbond_other	1.069
r_nbd_other	0.234
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.203
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.097
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3922
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	189

Software

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