8AWK

Structure of recombinant human beta-glucocerebrosidase in complex with D-carbaxylosyl chloride

X-RAY DIFFRACTION

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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
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.277	α = 90
b = 76.465	β = 102.047
c = 68.469	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		2020-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979499	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.58	52.158	100	0.143	0.998	8.8	6.7		73542

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.61			1.569	0.563	1.1

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	6TN1	1.58	52.158	73507	3644	99.929	0.153	0.1515	0.1849	19.369

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]
0.979		0.81	0.23		-1.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.482
r_dihedral_angle_4_deg	19.414
r_dihedral_angle_3_deg	13.163
r_dihedral_angle_1_deg	7.422
r_lrange_it	5.179
r_lrange_other	5.178
r_scangle_it	2.814
r_scangle_other	2.814
r_scbond_it	1.913
r_scbond_other	1.912
r_mcangle_it	1.717
r_mcangle_other	1.717
r_angle_refined_deg	1.551
r_angle_other_deg	1.392
r_mcbond_it	1.171
r_mcbond_other	1.17
r_nbd_refined	0.214
r_nbd_other	0.195
r_symmetry_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.183
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.156
r_metal_ion_refined	0.11
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.078
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3926
Nucleic Acid Atoms
Solvent Atoms	547
Heterogen Atoms	187

Software

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