#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes Authors: Landthaler, M. / Shub, D.A.
Resolution: 3.6→3.73 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.372 / % possible all: 99.7
-
Processing
Software
Name
Version
Classification
CNS
1.1
refinement
HKL-2000
datareduction
HKL-2000
datascaling
DM
phasing
Refinement
Method to determine structure: MIR / Resolution: 3.6→19.54 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 515958.48 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31
713
5 %
RANDOM
Rwork
0.277
-
-
-
all
0.277
15937
-
-
obs
0.277
14373
86.4 %
-
Displacement parameters
Biso mean: 142.4 Å2
Baniso -1
Baniso -2
Baniso -3
1-
9.04 Å2
0 Å2
0 Å2
2-
-
-22.67 Å2
0 Å2
3-
-
-
13.63 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.73 Å
0.62 Å
Luzzati d res low
-
20 Å
Luzzati sigma a
0.76 Å
0.58 Å
Refinement step
Cycle: LAST / Resolution: 3.6→19.54 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
4973
23
0
4996
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.007
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
1.3
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
17.4
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
1.53
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
LS refinement shell
Resolution: 3.6→3.82 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.388
98
4.9 %
Rwork
0.382
1891
-
obs
-
-
72.6 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
DNA-RNA_REP.PARAM
DNA-RNA.TOP
X-RAY DIFFRACTION
2
ION.PARAM
SPK.TOP
X-RAY DIFFRACTION
3
SPK.PARAM
ION.TOP
+
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