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Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4AMH
Influence of circular permutation on the folding pathway of a PDZ domain
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
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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
pH
7.5
Details
SITTING DROP VAPOR DIFFUSION, 0.1 M MES PH 6.0, 2.4 M AMMONIUM SULFATE
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 106.9
α = 90
b = 43.6
β = 103.7
c = 51.7
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
MARMOSAIC 225 mm CCD
PT COATED MIRRORS
2011-09-03
Diffraction Radiation
Monochromator
Protocol
SI (111) MONOCHROMATOR
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID23-2
--
ESRF
ID23-2
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
2.3
41.3
99.4
0.08
--
--
3.71
--
10415
--
2.1
32.75
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)
2.3
2.35
98.9
0.65
--
2.2
3.74
--
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
2.3
41.324
--
2.0
--
10415
521
99.46
--
0.222
0.2196
0.2683
--
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
2.3002
2.5316
--
127
2436
0.2898
0.4151
--
99.0
X Ray Diffraction
2.5316
2.8978
--
130
2461
0.2641
0.3048
--
100.0
X Ray Diffraction
2.8978
3.6506
--
129
2465
0.2294
0.3106
--
100.0
X Ray Diffraction
3.6506
41.3307
--
133
2529
0.1825
0.1926
--
99.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
40.37
Anisotropic B[1][1]
-10.1541
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-6.0282
Anisotropic B[2][2]
23.746
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-13.592
RMS Deviations
Key
Refinement Restraint Deviation
f_bond_d
0.008
f_plane_restr
0.004
f_chiral_restr
0.076
f_angle_d
1.264
f_dihedral_angle_d
15.658
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1386
Nucleic Acid Atoms
0
Heterogen Atoms
14
Solvent Atoms
53
Software
Software
Software Name
Purpose
PHENIX
refinement version: (PHENIX.REFINE)
XDS
data reduction
XSCALE
data scaling
PHASER
phasing