4HA3 | pdb_00004ha3

Structure of beta-glycosidase from Acidilobus saccharovorans in complex with Tris

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GOW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Protein solution (1.5mcl): 15mg/ml Asbeta-Gly, 0.025M NaCl, 0.05M Tris (pH 8.0). Reservoir solution (1.5mcl): 0.04M cellobiose, 0.16M magnesium acetate, 0.08M sodium cacodylate (pH 6.5), 16% w/v polyethylene glycol 8000, 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.18	α = 90
b = 84.18	β = 90
c = 166.22	γ = 90

Symmetry
Space Group	P 42 21 2

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	MAR CCD 165 mm		2010-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.9779	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.46	19.841	98	0.063	26.8		102050	102050			20.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.55	91.1		0.519	4.5		15340

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 (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	1gow	1.46	19.841	96870	5109	97.96	0.14394	0.14314	0.15	0.15886	0.17	RANDOM	14.262

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]
-0.26			-0.26		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.266
r_dihedral_angle_4_deg	16.422
r_dihedral_angle_3_deg	11.759
r_dihedral_angle_1_deg	6.175
r_scangle_it	3.081
r_scbond_it	1.975
r_angle_refined_deg	1.531
r_mcangle_it	1.337
r_angle_other_deg	0.882
r_mcbond_it	0.774

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.266
r_dihedral_angle_4_deg	16.422
r_dihedral_angle_3_deg	11.759
r_dihedral_angle_1_deg	6.175
r_scangle_it	3.081
r_scbond_it	1.975
r_angle_refined_deg	1.531
r_mcangle_it	1.337
r_angle_other_deg	0.882
r_mcbond_it	0.774
r_mcbond_other	0.228
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3906
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	38

Software

Software
Software Name	Purpose
AUTOMAR	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.