Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80% PEG 400, 100mM MOPS, 100mM NaNO3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
3
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
NSLS
X4A
1
0.97912,0.97947,0.96790,0.97930
SYNCHROTRON
NSLS
X4A
2
0.9793
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Apr 24, 2006
ADSC QUANTUM 4
2
CCD
May 9, 2006
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SI111CHANNEL
MAD
M
x-ray
1
2
SI111CHANNEL
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97912
1
2
0.97947
1
3
0.9679
1
4
0.9793
1
Reflection
D res high: 2.35 Å / D res low: 20 Å
Redundancy (%)
ID
Av σ(I) over netI
Number
Rmerge(I) obs
Χ2
Num. obs
% possible obs
4.2
1
13.1
164307
0.094
1.37
39303
99.6
4.2
2
11.6
162423
0.089
1.16
38883
99.7
3.5
3
6.8
136808
0.088
1.13
39588
99.7
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
6.31
20
94.5
1
0.076
2.471
3.8
5.04
6.31
98.9
1
0.082
2.002
4.1
4.41
5.04
99.3
1
0.077
2.048
4
4.01
4.41
99.8
1
0.076
2.007
4.1
3.72
4.01
99.9
1
0.075
1.813
4.2
3.51
3.72
99.8
1
0.077
1.565
4.2
3.33
3.51
99.9
1
0.086
1.528
4.3
3.19
3.33
99.9
1
0.093
1.326
4.3
3.06
3.19
100
1
0.104
1.219
4.3
2.96
3.06
100
1
0.116
1.18
4.3
2.87
2.96
100
1
0.133
1.162
4.3
2.79
2.87
100
1
0.173
1.104
4.3
2.71
2.79
99.9
1
0.183
1.05
4.3
2.65
2.71
99.9
1
0.229
1.037
4.3
2.59
2.65
100
1
0.219
0.989
4.3
2.53
2.59
100
1
0.264
1.033
4.2
2.48
2.53
99.9
1
0.3
1.014
4.2
2.43
2.48
99.9
1
0.36
1.045
4.1
2.39
2.43
100
1
0.363
1.021
4.1
2.35
2.39
100
1
0.443
1.02
4
6.31
20
95
2
0.068
1.731
4
5.04
6.31
99.7
2
0.065
1.428
4.2
4.41
5.04
99.9
2
0.066
1.662
4.2
4.01
4.41
99.9
2
0.067
1.632
4.2
3.72
4.01
99.9
2
0.067
1.405
4.3
3.51
3.72
99.9
2
0.072
1.277
4.3
3.33
3.51
99.9
2
0.085
1.196
4.3
3.19
3.33
100
2
0.098
1.073
4.3
3.06
3.19
99.9
2
0.118
1.021
4.3
2.96
3.06
100
2
0.141
1.029
4.3
2.87
2.96
100
2
0.161
0.983
4.3
2.79
2.87
100
2
0.231
0.996
4.3
2.71
2.79
99.9
2
0.26
0.987
4.3
2.65
2.71
99.9
2
0.33
0.997
4.2
2.59
2.65
99.9
2
0.351
0.972
4.1
2.53
2.59
100
2
0.41
0.969
4.1
2.48
2.53
99.9
2
0.436
0.974
4
2.43
2.48
99.9
2
0.625
0.958
3.9
2.39
2.43
99.9
2
0.576
0.94
3.9
2.35
2.39
99.9
2
0.705
0.96
3.9
6.31
20
97.7
3
0.05
1.766
3.2
5.04
6.31
99.4
3
0.064
1.458
3.4
4.41
5.04
99.8
3
0.062
1.53
3.4
4.01
4.41
99.9
3
0.071
1.595
3.5
3.72
4.01
99.9
3
0.089
1.456
3.5
3.51
3.72
99.9
3
0.112
1.255
3.6
3.33
3.51
99.9
3
0.141
1.109
3.6
3.19
3.33
99.9
3
0.195
1.058
3.6
3.06
3.19
100
3
0.256
1.009
3.6
2.96
3.06
99.9
3
0.344
1.011
3.6
2.87
2.96
99.9
3
0.447
0.993
3.6
2.79
2.87
99.9
3
0.681
0.987
3.6
2.71
2.79
100
3
0.746
0.954
3.5
2.65
2.71
99.9
3
0.963
3.5
2.59
2.65
99.8
3
0.93
3.4
2.53
2.59
99.7
3
0.941
3.4
2.48
2.53
99.6
3
0.916
3.3
2.43
2.48
99.2
3
0.891
3.3
2.39
2.43
99.4
3
0.889
3.2
2.35
2.39
99.2
3
0.938
3.1
Reflection
Resolution: 2.7→50 Å / Num. obs: 23521 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.8
Reflection shell
Resolution: 2.7→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.394 / % possible all: 93.2
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SnB
phasing
RESOLVE
phasing
CNS
refinement
PDB_EXTRACT
2
dataextraction
ADSC
datacollection
Refinement
Method to determine structure: MAD / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.295
1862
7.6 %
RANDOM
Rwork
0.275
-
-
-
obs
0.275
20535
83.4 %
-
all
-
24620
-
-
Solvent computation
Bsol: 43.91 Å2
Displacement parameters
Biso mean: 40.81 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.874 Å2
0 Å2
-8.638 Å2
2-
-
-8.554 Å2
0 Å2
3-
-
-
12.428 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2769
0
0
10
2779
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
1.054
1.5
X-RAY DIFFRACTION
c_mcangle_it
1.813
2
X-RAY DIFFRACTION
c_scbond_it
2.077
2
X-RAY DIFFRACTION
c_scangle_it
3.051
2.5
Refine LS restraints NCS
NCS model details: RESTRAINED
LS refinement shell
Resolution: 2.7→2.72 Å / Total num. of bins used: 37 /
Rfactor
Num. reflection
Rfree
0.352
29
Rwork
0.303
436
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PROTEIN_REP.PAR
protein.top
X-RAY DIFFRACTION
2
WATER_REP.PARAM
water.top
+
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