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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
1OR7
Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA
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)
Biological Assembly 3 (gz) (S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
6
Temperature
277.0
Details
sodium formate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 140.05
α = 90
b = 56.9
β = 130.51
c = 104.98
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MARRESEARCH
--
2002-04-26
Diffraction Radiation
Monochromator
Protocol
Si 111
MAD
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X9A
.9792
NSLS
X9A
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
35
98.3
--
0.083
--
2.2
84266
82833
-3.0
-3.0
--
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)
2.0
2.07
92.3
--
0.359
3.6
3.0
4296
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
MAD
2.0
30.0
--
-3.0
--
40441
2134
100.0
0.1987
0.19879
0.19705
0.23149
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
2.0
2.052
--
165
2975
0.3
0.307
--
--
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
19.358
Anisotropic B[1][1]
0.8
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
1.1
Anisotropic B[2][2]
-0.27
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
0.91
RMS Deviations
Key
Refinement Restraint Deviation
r_mcangle_it
1.622
r_xyhbond_nbd_refined
0.221
r_nbtor_other
0.335
r_dihedral_angle_3_deg
16.498
r_xyhbond_nbd_other
0.331
r_symmetry_vdw_other
0.319
r_angle_refined_deg
1.484
r_mcbond_it
0.845
r_nbd_other
0.227
r_bond_refined_d
0.015
r_gen_planes_other
0.007
r_chiral_restr
0.08
r_gen_planes_refined
0.008
r_symmetry_hbond_other
0.009
r_symmetry_hbond_refined
0.186
r_scbond_it
2.884
r_symmetry_vdw_refined
0.201
r_nbd_refined
0.257
r_scangle_it
4.766
r_angle_other_deg
1.125
r_dihedral_angle_1_deg
4.159
r_bond_other_d
0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3808
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
175
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.0
DENZO
data reduction
SCALEPACK
data scaling
MLPHARE
phasing