Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
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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: 2.150221 Å3/Da / Density % sol: 42.79657 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: Protein solution: protein 10mg/ml, 50 mM Tris pH 8.0, 5 mM MgCl2, 50 mM KCl, 0.1 mM EDTA Precipitant solution: 30% ethylene glycol, 0.1 M MES pH 6.0, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution: 1.81→1.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / Num. unique all: 64759 / Rsym value: 0.48 / % possible all: 52.3
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Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
MLPHARE
phasing
CNS
1
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MIR Starting model: Original modeling Resolution: 1.81→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The diffraction images were affected by the severe ice rings whose removal resulted in a loss of ~12% of the measured reflections from the refinement. the perfect merohedral twinning was ...Details: The diffraction images were affected by the severe ice rings whose removal resulted in a loss of ~12% of the measured reflections from the refinement. the perfect merohedral twinning was detected in the crystals with the twinning operator {h,-k,-l}. the refinement statistics presented for this entry corresponds to the refinement carried out using the twinning option of the cns program. for the deposition the diffraction data were detwinned using the cns program. therefore, the refinement statistics calculated based on the detwinned data might be slightly different from those obtained during the "twinned" refinement included in this entry.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.256
3150
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Random
Rwork
0.215
-
-
-
all
0.218
64759
-
-
obs
0.218
64759
80 %
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Displacement parameters
Biso mean: 40.83 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.29 Å
0.26 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.29 Å
0.28 Å
Refinement step
Cycle: LAST / Resolution: 1.81→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6082
0
4
479
6565
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.012
X-RAY DIFFRACTION
c_angle_deg
1.98
X-RAY DIFFRACTION
c_improper_angle_d
1.16
LS refinement shell
Resolution: 1.81→1.87 Å
Rfactor
Num. reflection
% reflection
Rfree
0.33
226
-
Rwork
0.328
-
-
obs
-
4486
52.3 %
+
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