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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4A6A
A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberculosis in complex with dTTP
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly 1 (gz) (A+S)
Biological Assembly 2 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
pH
7.5
Details
pH 7.5
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 56.59
α = 90
b = 179.51
β = 96.28
c = 99.81
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC CCD
FOCUSSING MIRRORS
2010-03-12
Diffraction Radiation
Monochromator
Protocol
CHANNEL CUT ESRF MONOCHROMATOR
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID14-4
--
ESRF
ID14-4
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
2.9
99
98.7
0.18
--
--
3.74
--
43288
--
0.0
--
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
OTHER
2.9
49.42
--
--
--
41123
2165
100.0
--
0.25478
0.25297
0.28985
RANDOM
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
2.9
2.975
--
162
3077
0.356
0.394
--
100.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
45.666
Anisotropic B[1][1]
-0.45
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-0.05
Anisotropic B[2][2]
0.3
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
0.15
RMS Deviations
Key
Refinement Restraint Deviation
r_angle_refined_deg
1.613
r_dihedral_angle_3_deg
16.347
r_mcangle_it
1.548
r_dihedral_angle_2_deg
29.887
r_scbond_it
2.006
r_scangle_it
3.721
r_dihedral_angle_1_deg
6.45
r_bond_refined_d
0.015
r_mcbond_it
0.779
r_chiral_restr
0.095
r_gen_planes_refined
0.006
r_dihedral_angle_4_deg
17.318
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
17538
Nucleic Acid Atoms
0
Heterogen Atoms
362
Solvent Atoms
12
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.5.0102
XDS
data reduction
XSCALE
data scaling