6YTR

Structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol aziridine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.155	α = 90
b = 156.779	β = 102.116
c = 68.23	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 X 16M		2021-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9762	Diamond	I02

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	1.7	66.799	99.9	0.159	0.064	0.994	6.3	6.6		119361

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	1.7	1.73	99.7		1.83	1.07	0.547	1

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	2NT0	1.7	66.799	119361	5927	99.883	0.161	0.1592	0.2026	24.919

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]
0.659		0.144	0.625		-1.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_1_deg	48.62
r_dihedral_angle_2_deg	33.948
r_dihedral_angle_4_deg	19.2
r_dihedral_angle_3_deg	13.438
r_dihedral_angle_1_deg	7.497
r_lrange_it	5.163
r_lrange_other	5.162
r_scangle_it	3.628
r_scangle_other	3.628
r_scbond_it	2.57
r_scbond_other	2.57
r_mcangle_it	2.301
r_mcangle_other	2.3
r_mcbond_it	1.704
r_mcbond_other	1.704
r_angle_refined_deg	1.591
r_angle_other_deg	1.372
r_nbd_other	0.31
r_symmetry_nbd_refined	0.245
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.209
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.163
r_symmetry_xyhbond_nbd_other	0.108
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7833
Nucleic Acid Atoms
Solvent Atoms	877
Heterogen Atoms	360

Software

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