Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 9
-
Sample preparation
Crystal
Density Matthews: 1.88 Å3/Da / Density % sol: 34.42 %
Crystal grow
Method: small tubes / pH: 6 Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc ...Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc sulfate) at 315K. The solution is then rapidly quenched to 293K by immersing it in a cool water bath. Quenching speed determines the resulting crystal size. 20-micron crystals are obtained by quenching in a 293K water bath, 10-micron crystals by quenching in a 283K water bath, and 5-micron crystals by quenching in ice water. pH 6.0, SMALL TUBES
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
3
100
1
4
100
1
1,2,3,4
1
Diffraction source
Source
Site
Beamline
ID
Wavelength
SYNCHROTRON
NSLS
X12B
1
1.28
SYNCHROTRON
NSLS
X12C
2
1.28
SYNCHROTRON
NSLS
X25
3
1.28
SYNCHROTRON
APS
23-ID-D
4
0.9733
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Apr 29, 2010
ADSC QUANTUM 210
2
CCD
Jul 30, 2010
ADSC QUANTUM 315
3
CCD
Feb 27, 2010
MARMOSAIC 300 mm CCD
4
CCD
Dec 19, 2009
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
3
SINGLEWAVELENGTH
M
x-ray
1
4
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.28
1
2
0.9733
1
Reflection
Resolution: 1.8→50 Å / Num. all: 7783 / Num. obs: 7770 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 62.2
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Processing
Software
Name
Version
Classification
CBASS
datacollection
SHELXS
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD Starting model: PDB ENTRY 4INS
Resolution: 1.8→40.85 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.454 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22311
357
4.6 %
RANDOM
Rwork
0.18135
-
-
-
obs
0.18338
7413
99.83 %
-
all
-
7783
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 37.509 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.18 Å2
0.09 Å2
0 Å2
2-
-
0.18 Å2
0 Å2
3-
-
-
-0.27 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→40.85 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
806
0
2
46
854
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
889
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.784
1.963
1220
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.773
5
115
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.003
24.667
45
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.954
15
145
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
8.064
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.134
0.2
134
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
697
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.37
1.5
534
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.626
2
864
X-RAY DIFFRACTION
r_scbond_it
3.423
3
355
X-RAY DIFFRACTION
r_scangle_it
5.716
4.5
348
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.435
24
-
Rwork
0.314
511
-
obs
-
-
97.81 %
+
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