1W18 | pdb_00001w18

Crystal Structure of levansucrase from Gluconacetobacter diazotrophicus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		0.5M AS, 30% ETHANOL, 0.1M NA-CITRATE PH5.6, pH 5.60

Crystal Properties
Matthews coefficient	Solvent content
3	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.803	α = 90
b = 119.391	β = 90
c = 215.101	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	ADSC CCD		2001-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.5	51.98	99.2	0.08	6.9	3.3		48568		2

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	2.5	2.64	98.5		0.32	2	3.2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OYG	2.5	105.41	46069	2444	99	0.2	0.197	0.21	0.25	RANDOM	24.33

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]
-2.06			4.57		-2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.555
r_dihedral_angle_4_deg	22.644
r_dihedral_angle_3_deg	18.132
r_dihedral_angle_1_deg	7.656
r_scangle_it	1.92
r_angle_refined_deg	1.509
r_scbond_it	1.232
r_angle_other_deg	0.886
r_mcangle_it	0.786
r_mcbond_it	0.612
r_symmetry_hbond_refined	0.28
r_symmetry_vdw_other	0.219
r_nbd_refined	0.209
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.143
r_nbtor_other	0.09
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7635
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing