8AWR | pdb_00008awr

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

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, 0.25M HEPES, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.111	α = 90
b = 76.48	β = 101.957
c = 68.147	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	1.49	51.96	98.9	0.104	0.997	8.6	6.7		85933

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	1.49	1.52			1.673	0.608	0.9

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	1.49	51.96	85814	4206	98.616	0.185	0.1834	0.185	0.2216	0.2238	22.777

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]
1.032		0.667	0.492		-1.658

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.432
r_dihedral_angle_4_deg	17.366
r_dihedral_angle_3_deg	12.864
r_dihedral_angle_1_deg	7.021
r_lrange_it	4.661
r_scangle_it	2.293
r_scbond_it	1.565
r_mcangle_it	1.449
r_angle_refined_deg	1.215
r_mcbond_it	0.972
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.22
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.156
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.128
r_chiral_restr	0.092
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3922
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	208

Software

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