Mass: 18.015 Da / Num. of mol.: 5 / 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: 1
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Sample preparation
Crystal
Density Matthews: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal grow
Temperature: 285 K / Method: vapor diffusion, sitting drop Details: A solution containing 18.9 mg/mL His6-tagged SuiB in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small clusters ...Details: A solution containing 18.9 mg/mL His6-tagged SuiB in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small clusters of crystals were formed within 24 hrs. A seed stock was then produced by combining a single sitting well with 10 uL of reservoir solution and 10 uL of enzyme at 8 mg/mL, followed by brief vortexing. A resulting crystal was harvested 2 days following seeding. The precipitant solution was 100 mM MES, pH 6.0, 15% (w/v) PEG 3350.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0332 Å / Relative weight: 1
Reflection
Resolution: 2.5→29.51 Å / Num. obs: 37704 / % possible obs: 99.3 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.7
Reflection shell
Resolution: 2.5→2.6 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3965 / % possible all: 94.4
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Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
datareduction
XDS
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.5→29.509 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.71 Details: INITIAL DATASET USED FOR ANOMALOUS PHASING FROM IRON ATOMS COLLECTED AT 1.7369 A.
Rfactor
Num. reflection
% reflection
Rfree
0.2568
1781
4.73 %
Rwork
0.2166
-
-
obs
0.2184
37648
99.31 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 2.5→29.509 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6725
0
48
5
6778
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
6945
X-RAY DIFFRACTION
f_angle_d
0.659
9433
X-RAY DIFFRACTION
f_dihedral_angle_d
12.409
2523
X-RAY DIFFRACTION
f_chiral_restr
0.022
1095
X-RAY DIFFRACTION
f_plane_restr
0.002
1187
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.498-2.5655
0.387
125
0.3735
2493
X-RAY DIFFRACTION
92
2.5655-2.6409
0.3946
131
0.3455
2743
X-RAY DIFFRACTION
100
2.6409-2.7261
0.3881
149
0.3362
2737
X-RAY DIFFRACTION
100
2.7261-2.8235
0.3428
118
0.3156
2751
X-RAY DIFFRACTION
100
2.8235-2.9364
0.3404
141
0.2956
2723
X-RAY DIFFRACTION
100
2.9364-3.0699
0.3463
147
0.2739
2730
X-RAY DIFFRACTION
100
3.0699-3.2316
0.3097
130
0.2748
2791
X-RAY DIFFRACTION
100
3.2316-3.4338
0.3217
134
0.2591
2734
X-RAY DIFFRACTION
100
3.4338-3.6984
0.2901
137
0.2307
2792
X-RAY DIFFRACTION
100
3.6984-4.0697
0.2546
141
0.2097
2782
X-RAY DIFFRACTION
100
4.0697-4.6567
0.2304
138
0.1745
2799
X-RAY DIFFRACTION
100
4.6567-5.8594
0.2108
140
0.1778
2828
X-RAY DIFFRACTION
100
5.8594-29.5105
0.1822
150
0.1657
2964
X-RAY DIFFRACTION
100
+
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