6YTP

Structure of recombinant human beta-glucocerebrosidase in complex with azide tagged cyclophellitol epoxide 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	4.6	291	1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.89	α = 90
b = 285.769	β = 90
c = 91.674	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		2016-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979490	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	68.202	99.9	0.077	0.036	0.999	12.1	5.5		156446

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			1.614	0.741	0.538	1.1	5.7

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	68.202	156420	7842	99.861	0.187	0.1859	0.2121	31.556

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]
4.941			-2.094		-2.848

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.868
r_dihedral_angle_other_1_deg	30.789
r_dihedral_angle_4_deg	19.613
r_dihedral_angle_3_deg	13.787
r_dihedral_angle_1_deg	7.293
r_lrange_other	6.01
r_lrange_it	6.009
r_scangle_it	4.009
r_scangle_other	4.009
r_mcangle_it	2.989
r_mcangle_other	2.989
r_scbond_other	2.57
r_scbond_it	2.569
r_mcbond_it	1.976
r_mcbond_other	1.975
r_angle_refined_deg	1.428
r_angle_other_deg	1.279
r_nbd_refined	0.206
r_symmetry_nbd_other	0.179
r_nbd_other	0.178
r_symmetry_nbd_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.071
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	7819
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	277

Software

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