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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Experiment
4K32
Crystal structure of geneticin bound to the leishmanial rRNA A-site
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 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
7
Temperature
293.15
Details
50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1-20% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-200 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 33.08
α = 90
b = 90.76
β = 90
c = 47.01
γ = 90
Symmetry
Space Group
P 21 21 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315r
--
--
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID14-4
0.9394
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
2.5
50
81.6
0.046
--
--
--
21134
4294
21.5
21.5
--
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
2.5
2.57
84.7
0.64
--
2.0
--
--
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
MOLECULAR REPLACEMENT
2.5
23.505
--
2.04
4290
4290
429
81.64
--
0.2096
0.2058
0.2445
--
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
2.5004
2.8616
--
143
1295
0.3186
0.3486
--
85.0
X Ray Diffraction
2.8616
3.6033
--
144
1300
0.2102
0.2987
--
83.0
X Ray Diffraction
3.6033
23.506
--
142
1266
0.1768
0.1956
--
77.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
1.5826
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-7.1484
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
5.5658
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
16.821
f_plane_restr
0.008
f_bond_d
0.006
f_angle_d
0.954
f_chiral_restr
0.057
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
0
Nucleic Acid Atoms
898
Heterogen Atoms
68
Solvent Atoms
11
Software
Software
Software Name
Purpose
DNA
data collection
PHASER
phasing
PHENIX
refinement version: (phenix.refine: 1.6.1_357)
XDS
data reduction
XDS
data scaling