3BYL

Crystal structure of B. subtilis levansucrase mutant E342A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6.3	291	diammonium phosphate, sodium acetate, pH 6.3, MICRODIALYSIS, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.133	α = 90
b = 67.281	β = 90
c = 123.622	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	MAC Science DIP-2030		2003-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.07	30	98.8	0.037	0.037	25	4.5	26368	26368

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.14	98.8		0.068	0.068	25.1	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1OYG	2.1	30	25331	25331	1286	98.87	0.182	0.182	0.18	0.222	RANDOM	13.689

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]
-0.62			0.75		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.795
r_scangle_it	1.777
r_angle_refined_deg	1.207
r_scbond_it	1.155
r_angle_other_deg	0.771
r_mcangle_it	0.62
r_mcbond_it	0.341
r_symmetry_vdw_other	0.318
r_symmetry_vdw_refined	0.31
r_symmetry_hbond_refined	0.24
r_nbd_other	0.238
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.081
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3438
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling