Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE FOR 1QMT PDB CORRESPONDS TO RECOMBINANT HUMAN ECP. IT INCLUDES THE COMPLETE NATIVE PROTEIN ...SEQUENCE FOR 1QMT PDB CORRESPONDS TO RECOMBINANT HUMAN ECP. IT INCLUDES THE COMPLETE NATIVE PROTEIN AND AN ADDITIONAL MET AT THE N-TERMINAL. THE NATIVE ECP (RESIDUES 1 -133) CORRESPONDS TO RESIDUES 28-160 OF THE ECP PRECURSOR (SWS P12724). RESIDUES 1-27 OF P12724 ARE THE SIGNAL PEPTIDE.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.3 Å3/Da / Density % sol: 53.2 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.4→40 Å / Num. obs: 6916 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.93 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7
Reflection shell
Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.5 / % possible all: 65
Reflection
*PLUS
Num. measured all: 34137
Reflection shell
*PLUS
% possible obs: 65 %
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Processing
Software
Name
Version
Classification
X-PLOR
3.851
refinement
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
3.851
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: EOSINOPHIL DERIVED NEUROTOXIN STRUCTURE AT 1.8 ANGSTROMS (COORDINATES NOT SUBMITTED) WAS PROVIDED BY S.MOSIMANN AND M.N.G.JAMES AND USED FOR MOLECULAR REPLACEMENT. Resolution: 2.4→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.229
552
8 %
RANDOM
Rwork
0.176
-
-
-
obs
0.176
6907
95.4 %
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Displacement parameters
Biso mean: 38.8 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.32 Å
0.27 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.34 Å
0.38 Å
Refinement step
Cycle: LAST / Resolution: 2.4→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1102
0
0
27
1129
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.01
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.5
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
28.1
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
0.78
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
2.28
1.5
X-RAY DIFFRACTION
x_mcangle_it
3.75
2
X-RAY DIFFRACTION
x_scbond_it
4.15
2
X-RAY DIFFRACTION
x_scangle_it
6.38
2.5
LS refinement shell
Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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