9J4Q | pdb_00009j4q

Crystal structure of glucose bound covalent intermediate of GH1 beta-glucosidase (UnBGl1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9J3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	295	0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.2	α = 90
b = 65.8	β = 90
c = 137.9	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	IMAGE PLATE	RIGAKU RAXIS IV++		2019-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	30	98.8	0.907	6.95	3.7		31988

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	97.6		0.562	2.04

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	29.69	30390	1600	99.06	0.18792	0.18563	0.1946	0.23157	0.2413	RANDOM	29.731

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			1.23		-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.013
r_dihedral_angle_2_deg	7.239
r_dihedral_angle_1_deg	6.869
r_long_range_B_refined	5.81
r_long_range_B_other	5.809
r_scangle_other	4.083
r_mcangle_it	2.986
r_mcangle_other	2.986
r_scbond_it	2.809
r_scbond_other	2.801
r_mcbond_it	2.192
r_mcbond_other	2.192
r_angle_refined_deg	1.549
r_angle_other_deg	0.541
r_chiral_restr	0.073
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
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	3564
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing