- PDB-3f82: Crystal structure of the tyrosine kinase domain of the hepatocyte... -
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Basic information
Entry
Database: PDB / ID: 3f82
Title
Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-MET in complex with N-(4-(2-amino-3-chloropyridin-4-yloxy)-3-fluorophenyl)-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.5→25 Å / Num. obs: 11610 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 39.628 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.3
Reflection shell
Resolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.2 / % possible all: 97.2
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Processing
Software
Name
Version
Classification
AMoRE
phasing
BUSTER-TNT
2.5.1
refinement
HKL-2000
(DENZO)
datareduction
HKL-2000
(SCALEPACK)
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: MET KINASE COMPLEXED WITH BMS-758982 Resolution: 2.5→16.54 Å / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2533
547
4.79 %
RANDOM
Rwork
0.18
-
-
-
all
0.1834
11431
-
-
obs
0.1834
11431
99.31 %
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Displacement parameters
Biso mean: 30.91 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.44456646 Å2
0 Å2
0 Å2
2-
-
-0.2538769 Å2
0 Å2
3-
-
-
-3.19068956 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→16.54 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2169
0
36
127
2332
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Weight
X-RAY DIFFRACTION
t_bond_d
0.006
2261
2
X-RAY DIFFRACTION
t_angle_deg
0.868
3054
2
X-RAY DIFFRACTION
t_dihedral_angle_d
21.361
422
0
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
0.006
40
2
X-RAY DIFFRACTION
t_gen_planes
0.01
326
5
X-RAY DIFFRACTION
t_it
1.319
2261
20
X-RAY DIFFRACTION
t_nbd
0.032
29
5
LS refinement shell
Resolution: 2.5→2.65 Å / Total num. of bins used: 9
Rfactor
Num. reflection
% reflection
Rfree
0.2578
80
4.54 %
Rwork
0.1825
1682
-
all
0.186
1762
-
obs
-
-
99.31 %
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