Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2009 Details: The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror.
Radiation
Monochromator: a double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 3.01→3.12 Å / Redundancy: 6.67 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1 / Num. unique all: 12 / Rsym value: 0.352 / % possible all: 100
-
Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
PHASER
phasing
REFMAC
5.5.0109
refinement
AUTOMAR
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Z-type DNA Dinucleotide step built using InsightII Resolution: 3.01→15.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.835 / SU B: 16.392 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND COMPRISES OF A DINUCLEOTIDE STEP ...Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND COMPRISES OF A DINUCLEOTIDE STEP IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE DINUCLEOTIDE STEP COULD STAND FOR EITHER CPG/CPG OR CPA/TPG. DUE TO DISORDER, THE DINUCLEOTIDE STEP WAS CONSTRUCTED AS TPG/TPG WHERE THE C5 METHYL GROUP OF THYMINE WAS ASSIGNED OCCUPANCY OF 1/6 AND N2 OF GUANINE WAS ASSIGNED OCCUPANCY OF 5/6.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23283
10
6.9 %
RANDOM
Rwork
0.19618
-
-
-
obs
0.19924
135
98.64 %
-
all
-
145
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 23.785 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.06 Å2
-0.03 Å2
0 Å2
2-
-
-0.06 Å2
0 Å2
3-
-
-
0.09 Å2
Refinement step
Cycle: LAST / Resolution: 3.01→15.15 Å /
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
81
0
1
82
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.021
89
X-RAY DIFFRACTION
r_angle_refined_deg
3.939
3
134
X-RAY DIFFRACTION
r_chiral_restr
0.181
0.2
15
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
44
X-RAY DIFFRACTION
r_scbond_it
2.307
3
89
X-RAY DIFFRACTION
r_scangle_it
3.726
4.5
134
LS refinement shell
Resolution: 3.013→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0
0
-
Rwork
0.384
8
-
obs
-
8
100 %
+
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