6YV3

Structure of recombinant human beta-glucocerebrosidase in complex with galacto-configured 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, HANGING DROP		291	1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.8

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.556	α = 90
b = 285.273	β = 90
c = 91.83	γ = 90

Symmetry
Space Group	C 2 2 21

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		2016-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979500	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	1.8	72.197	100	0.116	0.052	0.998	10.9	5.9		134042

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	1.83	100		1.364	0.848	0.59	1.2	5.8

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	2NT0	1.8	72.197	134017	6677	99.884	0.177	0.1755	0.2032	28.029

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]
3.874			-1.618		-2.257

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.465
r_dihedral_angle_4_deg	17.405
r_dihedral_angle_3_deg	13.623
r_dihedral_angle_1_deg	7.172
r_lrange_it	6.299
r_lrange_other	6.299
r_scangle_it	4.219
r_scangle_other	4.219
r_mcangle_it	2.914
r_mcangle_other	2.914
r_scbond_it	2.638
r_scbond_other	2.638
r_mcbond_it	1.871
r_mcbond_other	1.87
r_dihedral_angle_other_1_deg	1.632
r_angle_refined_deg	1.443
r_angle_other_deg	1.295
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.204
r_nbd_other	0.201
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.026
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7791
Nucleic Acid Atoms
Solvent Atoms	855
Heterogen Atoms	269

Software

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