6TJK | pdb_00006tjk

Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2 M Na2SO4, 14% (v/v) PEG3350, 0.1 M bis-tris-propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.744	α = 90
b = 156.222	β = 102.473
c = 68.264	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 X 16M		2019-07-19	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	1.56	66.742	99.4	0.105	0.057	0.987	7.4	4.3		147746

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	1.56	1.59			1.67	0.901	0.336	0.7

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	6Q6K	1.56	66.742	147674	7465	96.714	0.166	0.1646	0.18	0.1985	0.21	22.553

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]
1.457		0.66	-0.632		-1.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.465
r_dihedral_angle_4_deg	18.972
r_dihedral_angle_3_deg	13.019
r_dihedral_angle_1_deg	7.472
r_lrange_it	4.783
r_lrange_other	4.779
r_scangle_it	3.369
r_scangle_other	3.368
r_scbond_it	2.37
r_scbond_other	2.37
r_mcangle_it	2.15
r_mcangle_other	2.15
r_angle_refined_deg	1.588
r_mcbond_it	1.579
r_mcbond_other	1.576
r_angle_other_deg	1.394
r_nbd_other	0.236
r_nbd_refined	0.214
r_symmetry_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.181
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.171
r_chiral_restr_other	0.166
r_symmetry_nbd_refined	0.149
r_symmetry_nbtor_other	0.094
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7833
Nucleic Acid Atoms
Solvent Atoms	895
Heterogen Atoms	411

Software

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