5FJS | pdb_00005fjs

Bacterial beta-glucosidase reveals the structural and functional basis of genetic defects in human glucocerebrosidase 2 (GBA2)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BVU	PDB ENTRY 5BVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 8, 15 % W/V PEG 6000.

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.974	α = 90
b = 187.974	β = 90
c = 99.075	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PIXEL		2014-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	45.1	100	0.11	15.9	10.3		61406		1.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	100		1.32	1.7	10.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 5BVU	2.6	162.61	58306	3081	99.97	0.20862	0.20559	0.21	0.26649	0.27	RANDOM	58.022

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]
-0.54	-0.27		-0.54		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.929
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	15.838
r_long_range_B_refined	8.36
r_long_range_B_other	8.354
r_dihedral_angle_1_deg	7.054
r_mcangle_it	6.594
r_mcangle_other	6.593
r_scangle_other	6.235
r_mcbond_it	4.476
r_mcbond_other	4.475
r_scbond_it	4.208
r_scbond_other	4.208
r_angle_refined_deg	1.561
r_angle_other_deg	1.021
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11055
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	2

Software

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