6TJQ | pdb_00006tjq

Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TJK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.112	α = 90
b = 76.351	β = 101.987
c = 68.16	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		2019-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.41	51.95	100	0.135	0.056	0.999	7.2	6.7		102363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	7.72			2.388	0.357	0.4

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	6TJK	1.41	51.95	102326	4992	99.9	0.179	0.1776	0.18	0.2053	0.21	20.829

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]
0.462		0.748	1.266		-1.876

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.684
r_dihedral_angle_4_deg	20.58
r_dihedral_angle_1_deg	18.896
r_dihedral_angle_3_deg	13.019
r_lrange_it	4.66
r_lrange_other	4.399
r_scangle_it	2.596
r_scangle_other	2.595
r_scbond_it	1.742
r_scbond_other	1.741
r_mcangle_it	1.637
r_mcangle_other	1.637
r_angle_refined_deg	1.461
r_angle_other_deg	1.358
r_mcbond_it	1.136
r_mcbond_other	1.136
r_nbd_other	0.234
r_nbd_refined	0.208
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.172
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.164
r_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3923
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	177

Software

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