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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
2XKW
LIGAND BINDING DOMAIN OF HUMAN PPAR-GAMMA IN COMPLEX WITH THE AGONIST PIOGLITAZONE
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
PROTEIN CONC. 17MG/ML, 50 MM TRIS PH 8.0,0.1M NACL, 0.5 MM DTT, 2 MM EDTA. RESERVOIR: 20% PEG4000,10% ISOPROPANOL, 0.1M HEPES PH 7.5 , VAPOR DIFFUSION,TEMPERATURE 292K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 92.86
α = 90
b = 60.41
β = 103.01
c = 119.85
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
IMAGE PLATE
MARRESEARCH
MIRRORS
2005-01-18
Diffraction Radiation
Monochromator
Protocol
SI-111 CRYSTAL
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
BESSY BEAMLINE 14.2
--
BESSY
14.2
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
2.01
20
97.2
0.04
--
--
3.1
--
39168
--
0.0
34.8
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)
2.01
2.08
63.1
0.29
--
2.5
2.4
--
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
2.02
20.0
--
0.0
--
39168
2104
97.2
--
0.164
0.162
0.202
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
2.02
2.09
--
169
3067
0.201
0.285
--
78.85
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
33.61
Anisotropic B[1][1]
-0.82
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.09
Anisotropic B[2][2]
2.2
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-1.34
RMS Deviations
Key
Refinement Restraint Deviation
r_gen_planes_refined
0.005
r_symmetry_hbond_refined
0.101
r_scangle_it
11.83
r_dihedral_angle_2_deg
37.686
r_angle_other_deg
0.939
r_nbd_refined
0.217
r_mcangle_it
5.959
r_nbtor_refined
0.181
r_scbond_it
9.432
r_nbtor_other
0.085
r_mcbond_it
4.856
r_chiral_restr
0.105
r_gen_planes_other
0.001
r_symmetry_vdw_refined
0.205
r_symmetry_vdw_other
0.178
r_dihedral_angle_4_deg
16.245
r_dihedral_angle_1_deg
5.199
r_angle_refined_deg
1.36
r_mcbond_other
1.66
r_xyhbond_nbd_refined
0.132
r_dihedral_angle_3_deg
15.56
r_bond_refined_d
0.012
r_nbd_other
0.163
r_bond_other_d
0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
4145
Nucleic Acid Atoms
0
Heterogen Atoms
78
Solvent Atoms
182
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.2.0005
HKL-2000
data reduction
SCALEPACK
data scaling
PHASER
phasing