Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 4
-
Sample preparation
Crystal
Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.3M Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
3
100
1
4
100
1
Diffraction source
Source
Type
ID
Wavelength (Å)
ROTATING ANODE
OTHER
1
1.54
ROTATING ANODE
OTHER
2
1.54
ROTATING ANODE
OTHER
3
1.54
ROTATING ANODE
OTHER
4
1.54
Detector
Type
ID
Detector
Date
MAC Science DIP-2030
1
IMAGE PLATE
Aug 30, 1997
RIGAKU RAXIS II
2
IMAGE PLATE
Mar 4, 1998
RIGAKU RAXIS II
3
IMAGE PLATE
Mar 4, 1998
MAC Science DIP-2030
4
IMAGE PLATE
Mar 23, 1998
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
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 2.05→20 Å / Num. obs: 14738 / % possible obs: 99.7 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 0.443
Reflection shell
Resolution: 2.05→2.16 Å / Mean I/σ(I) obs: 16.7 / Rsym value: 0.153 / % possible all: 99.8
-
Processing
Software
Name
Version
Classification
NB
CNS
0.3
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
SCALEPACK
datascaling
CNS
phasing
Refinement
Method to determine structure: MIR / Resolution: 2.05→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1082751.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.242
737
5 %
RANDOM
Rwork
0.224
-
-
-
obs
-
14640
99.7 %
-
Displacement parameters
Biso mean: 27.5 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.19 Å2
0 Å2
0 Å2
2-
-
2.19 Å2
0 Å2
3-
-
-
-4.39 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.29 Å
0.26 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.18 Å
0.12 Å
Refinement step
Cycle: LAST / Resolution: 2.05→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1304
0
0
153
1457
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.007
X-RAY DIFFRACTION
c_angle_deg
1.6
X-RAY DIFFRACTION
c_dihedral_angle_d
26.7
X-RAY DIFFRACTION
c_improper_angle_d
0.75
LS refinement shell
Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.271
124
5.2 %
Rwork
0.226
2275
-
obs
-
2399
100 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
protein_rep.param
protein.top
X-RAY DIFFRACTION
2
water_rep.param
water.top
+
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