4HA4 | pdb_00004ha4

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Protein solution (1.5mcl): 13mg/ml Asbeta-Gly, 0.025M NaCl, 0.025M Hepes (pH 7.5). Reservoir solution (1.5mcl): 1.0M succinic acid (pH 7.0), 0.1M Hepes (pH 7.0), 1% w/v polyethylene glycol monomethyl ether 2000. The crystal was soaked in a cryoprotection solution containing 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.12	α = 90
b = 84.12	β = 90
c = 166.27	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	0.9815	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	1.37	19.827	98.8	0.063	17.2			124046			20.1

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	1.37	1.45	96.5		0.81	2.1		18722

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	1.37	19.827	117803	6243	98.83	0.13213	0.13049	0.1296	0.16333	0.1621	RANDOM	15.182

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]
-0.27			-0.27		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.875
r_dihedral_angle_4_deg	15.576
r_dihedral_angle_3_deg	12.343
r_sphericity_free	7.943
r_dihedral_angle_1_deg	6.226
r_scangle_it	3.974
r_sphericity_bonded	3.704
r_scbond_it	2.945
r_mcangle_it	2.075
r_angle_refined_deg	1.559
r_mcbond_it	1.478
r_rigid_bond_restr	1.387
r_angle_other_deg	0.927
r_mcbond_other	0.722
r_chiral_restr	0.114
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3909
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	72

Software

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