8AX3 | pdb_00008ax3

Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl fluoride

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
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.92	α = 90
b = 155.984	β = 101.964
c = 68.036	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		2020-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976230	Diamond	I03

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	1.59	51.99	99.6	0.135	0.997	8.6	6.9		994940

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	1.59	1.62			1.8	0.544	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8AWK	1.59	51.824	143489	7124	99.434	0.183	0.1819	0.19	0.2125	0.22	20.388

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]
1.471		0.406	-0.003		-1.504

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_1_deg	40.093
r_dihedral_angle_2_deg	34.284
r_dihedral_angle_4_deg	17.004
r_dihedral_angle_3_deg	13.142
r_dihedral_angle_1_deg	7.453
r_lrange_it	4.281
r_lrange_other	4.135
r_scangle_it	2.325
r_scangle_other	2.325
r_mcangle_it	1.693
r_mcangle_other	1.693
r_scbond_it	1.557
r_scbond_other	1.557
r_angle_refined_deg	1.417
r_angle_other_deg	1.302
r_mcbond_it	1.138
r_mcbond_other	1.137
r_nbd_other	0.232
r_metal_ion_refined	0.205
r_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.167
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.074
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	7845
Nucleic Acid Atoms
Solvent Atoms	893
Heterogen Atoms	400

Software

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