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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
1PUG
Structure of E. coli Ybab
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
Method
Vapor Diffusion
pH
7.5
Temperature
291.0
Details
1.9M Ammonium Sulfate 0.1MSodium HEPES pH 7.5 5% Ethylene Glycol, VAPOR DIFFUSION, temperature 291K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 63.87
α = 90
b = 84.24
β = 90
c = 86.64
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
MARRESEARCH
--
2003-05-28
Diffraction Radiation
Monochromator
Protocol
SAGITALLY FOCUSED Si(111)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 31-ID
0.9798
APS
31-ID
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
1.9
20
99.3
0.073
--
--
--
37158
36898
--
-0.5
--
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)
1.9
1.97
94.5
--
--
--
--
--
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
SIR
2.2
20.0
--
0.0
22948
22865
1177
99.64
--
0.21584
0.21211
0.28412
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
2.2
2.256
--
92
1605
0.237
0.298
--
--
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
63.383
Anisotropic B[1][1]
2.41
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-3.67
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
1.26
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_1_deg
8.222
r_scangle_it
6.845
r_symmetry_hbond_refined
0.414
r_nbd_other
0.267
r_symmetry_vdw_other
0.369
r_scbond_it
3.966
r_bond_refined_d
0.032
r_bond_other_d
0.002
r_mcangle_it
3.134
r_gen_planes_other
0.014
r_gen_planes_refined
0.012
r_mcbond_it
1.776
r_chiral_restr
0.142
r_angle_refined_deg
2.407
r_xyhbond_nbd_refined
0.23
r_nbd_refined
0.27
r_symmetry_vdw_refined
0.324
r_nbtor_other
0.104
r_angle_other_deg
1.187
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2492
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
163
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
SOLVE
phasing
RESOLVE
model building
REFMAC
refinement version: 5.1.24
RESOLVE
phasing