7NWV

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY Tagged Cyclophellitol 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	7	293	0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.956	α = 90
b = 158.42	β = 102.147
c = 68.238	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		2021-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.86	158.42	100	0.119	0.129	0.996	9.1	6.9		91928

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89			0.843	0.913	0.859	2

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	1.86	66.8	91876	4665	99.94	0.18	0.1769	0.2318	24.294

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]
0.347		0.087	1.848		-2.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_1_deg	37.453
r_dihedral_angle_2_deg	34.286
r_dihedral_angle_4_deg	20.072
r_dihedral_angle_3_deg	14.196
r_dihedral_angle_1_deg	7.478
r_lrange_it	4.949
r_lrange_other	4.949
r_scangle_it	3.437
r_scangle_other	3.437
r_scbond_it	2.404
r_scbond_other	2.403
r_mcangle_it	2.356
r_mcangle_other	2.355
r_mcbond_it	1.722
r_mcbond_other	1.722
r_angle_refined_deg	1.57
r_angle_other_deg	1.329
r_nbd_other	0.24
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7819
Nucleic Acid Atoms
Solvent Atoms	744
Heterogen Atoms	384

Software

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