6TN1 | pdb_00006tn1

Unliganded Crystal Structure of Recombinant GBA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NT1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Mg formate, 19% (v/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.451	α = 86.04
b = 46.176	β = 75.191
c = 64.209	γ = 82.782

Symmetry
Space Group	P 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 PILATUS 6M-F		2019-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	0.98	31.68	74.2	0.043	0.037	0.994	8.7	1.9		208682

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	0.98	1			0.486	0.486	0.685

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	2NT1	0.98	31.68	208659	9829	74.235	0.112	0.1116	0.14	0.1282	0.15	9.105

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]
0.239	0.025	-0.249	0.065	-0.348	-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.052
r_dihedral_angle_4_deg	18.453
r_dihedral_angle_3_deg	12.571
r_dihedral_angle_1_deg	6.998
r_lrange_it	2.461
r_lrange_other	2.405
r_angle_refined_deg	1.568
r_angle_other_deg	1.513
r_scangle_it	1.154
r_scangle_other	1.154
r_rigid_bond_restr	0.995
r_mcangle_it	0.937
r_mcangle_other	0.937
r_scbond_it	0.926
r_scbond_other	0.926
r_mcbond_it	0.663
r_mcbond_other	0.663
r_nbd_refined	0.266
r_symmetry_xyhbond_nbd_other	0.254
r_nbd_other	0.241
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.169
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.041
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3909
Nucleic Acid Atoms
Solvent Atoms	693
Heterogen Atoms	149

Software

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