9W4F | pdb_00009w4f

Crystal structure of beta-glucosidase CaBGL mutant E163Q in complex with glucose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		289	0.1M Bis-Tris, pH 6.5, 2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.03	α = 90
b = 221.58	β = 90
c = 236.72	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2019-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97911	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.26	36.92	100	0.071	0.077	0.03	0.998	17.7	6.8		339559

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.32		100	0.607	0.66	0.257	0.881		6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.26	36.9	322272	17163	99.94	0.20371	0.20266	0.207	0.2233	0.226	RANDOM	47.911

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]
-0.55			-1.66		2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.002
r_long_range_B_refined	9.802
r_long_range_B_other	9.802
r_scangle_other	7.658
r_mcangle_it	5.839
r_mcangle_other	5.839
r_dihedral_angle_1_deg	5.714
r_scbond_it	5.132
r_scbond_other	5.128
r_mcbond_it	4.292
r_mcbond_other	4.291
r_dihedral_angle_2_deg	4.226
r_angle_refined_deg	1.455
r_angle_other_deg	0.505
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	45436
Nucleic Acid Atoms
Solvent Atoms	960
Heterogen Atoms	330

Software

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