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139717
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
1IYI
Crystal structure of hematopoietic prostaglandin D synthase
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 Hanging Drop
pH
8.4
Temperature
293.0
Details
PEG6000, Tris-HCl, magnesium chloride, Glutathione, dioxan, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 48.78
α = 90
b = 47.26
β = 97.83
c = 183.81
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
IMAGE PLATE
RIGAKU RAXIS IV
--
1997-10-01
Diffraction Radiation
Monochromator
Protocol
diamond
MAD
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
1.0
SPring-8
BL41XU
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
1.8
37.29
94.06
--
--
--
6.08
444028
72996
1.0
1.0
11.3
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)
1.8
1.86
69.3
--
--
--
--
--
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
1.8
37.29
--
1.0
444028
72996
7397
94.0
--
0.188
0.188
0.22
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
1.8
1.91
--
982
8614
0.219
0.251
0.008
75.1
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
RESTRAINED
Mean Isotropic B
18.7
Anisotropic B[1][1]
4.8
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
2.25
Anisotropic B[2][2]
-3.32
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-1.48
RMS Deviations
Key
Refinement Restraint Deviation
c_improper_angle_d
0.73
c_angle_deg
1.1
c_dihedral_angle_d
20.4
c_bond_d
0.005
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.19
Luzzati Sigma A (Observed)
0.14
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.23
Luzzati Sigma A (R-Free Set)
0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
6552
Nucleic Acid Atoms
0
Heterogen Atoms
82
Solvent Atoms
1089
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
MLPHARE
phasing
CNS
refinement version: 1.0