9UPT | pdb_00009upt

Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio thermocellus

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, HANGING DROP	7.2	277.15	0.1 M HEPES pH 7.2, 10% 2-propanol, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.27	α = 90
b = 158.27	β = 90
c = 53.962	γ = 120

Symmetry
Space Group	P 6

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	RAYONIX MX300-HS		2019-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

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	2.369	79.26	98.3	0.999	10.9	1.9		31219

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	2.37	2.46	100		0.799

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	5OGZ	2.369	79.26	31219	1638	98.25	0.175	0.1727	0.1735	0.215	0.2161	47.407

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]
-1.263	-0.631		-1.263		4.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.541
r_dihedral_angle_6_deg	14.415
r_lrange_other	8.972
r_lrange_it	8.971
r_scangle_it	7.743
r_scangle_other	7.742
r_dihedral_angle_1_deg	6.977
r_dihedral_angle_2_deg	6.573
r_mcangle_it	5.485
r_mcangle_other	5.484
r_scbond_it	5.162
r_scbond_other	5.161
r_mcbond_it	3.96
r_mcbond_other	3.96
r_angle_refined_deg	1.787
r_angle_other_deg	0.616
r_nbd_refined	0.227
r_nbtor_refined	0.193
r_symmetry_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.151
r_nbd_other	0.14
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_symmetry_nbd_refined	0.043
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3641
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing