5IDI | pdb_00005idi

Structure of beta glucosidase 1A from Thermotoga neapolitana, mutant E349A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CBV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	288	Protein at 12 mg/ml in 20 mM citrate phosphate buffer, pH 5.6. Hanging drops consisting of 1 microlitre of protein solution and 2 microlitres of reservoir solution (18-23% w/v PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0) equilibrated against 1 ml of reservoir solution. Rod-shaped crystals of approximate dimensions 0.3 x 0.2 x 0.3 mm grew after 8-10 days.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.277	α = 90
b = 98.726	β = 90
c = 154.756	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	MARRESEARCH		2011-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.0402	MAX II	I911-2

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	1.9	30.1	99.1	0.084	12.6	5		81717

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	1.9	1.93	85.4		1.172	1.9

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	2CBV	1.9	30	77455	4096	98.85	0.17082	0.16857	0.18	0.2147	0.22	RANDOM	27.434

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]
1.04			-0.42		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.831
r_dihedral_angle_4_deg	21.985
r_dihedral_angle_3_deg	14.176
r_dihedral_angle_1_deg	6.696
r_long_range_B_refined	4.992
r_long_range_B_other	4.947
r_scangle_other	3.433
r_angle_refined_deg	2.24
r_scbond_it	2.202
r_scbond_other	2.202
r_mcangle_it	1.84
r_mcangle_other	1.84
r_mcbond_it	1.313
r_mcbond_other	1.283
r_angle_other_deg	1.191
r_chiral_restr	0.155
r_bond_refined_d	0.027
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	7300
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	12

Software

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