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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
4GYH
Structure of human thymidylate synthase at high salt conditions
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
8.5
Temperature
298.0
Details
100mM TRIS, 1.8M Ammonium Sulfate, 20mM 2-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 96.19
α = 90
b = 96.19
β = 90
c = 83.28
γ = 120
Symmetry
Space Group
P 31 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
173
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MAR scanner 345 mm plate
--
2011-10-26
Diffraction Radiation
Monochromator
Protocol
Si 111 CHANNEL
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU
1.5418
--
--
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
3
19.6
94.4
--
--
--
7.9
9141
8628
1.35
1.35
--
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)
3.0
3.1
97.6
--
--
--
--
--
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
3.005
19.632
--
1.34
10060
8628
869
94.39
--
0.2216
0.215
0.2802
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
3.005
3.1925
--
139
1278
0.3191
0.4121
--
95.0
X Ray Diffraction
3.1925
3.4378
--
156
1357
0.238
0.3015
--
100.0
X Ray Diffraction
3.4378
3.7815
--
107
950
0.316
0.4589
--
72.0
X Ray Diffraction
3.7815
4.3236
--
153
1358
0.2146
0.2704
--
99.0
X Ray Diffraction
4.3236
5.4282
--
158
1369
0.1608
0.2207
--
100.0
X Ray Diffraction
5.4282
19.6322
--
156
1447
0.1854
0.2251
--
100.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
-5.3941
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-5.3941
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
10.7883
RMS Deviations
Key
Refinement Restraint Deviation
f_bond_d
0.009
f_plane_restr
0.004
f_angle_d
1.212
f_chiral_restr
0.075
f_dihedral_angle_d
20.137
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2125
Nucleic Acid Atoms
0
Heterogen Atoms
10
Solvent Atoms
0
Software
Software
Software Name
Purpose
MAR345dtb
data collection
PHASER
phasing
PHENIX
refinement version: (phenix.refine: 1.7.1_743)
HKL-2000
data reduction
HKL-2000
data scaling