1ML1
PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OF A SEVEN RESIDUE LOOP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TTJ | PDB ENTRY 1TTJ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | PLEASE SEE JRNL ARTICLE, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 165.23 | α = 90 |
b = 165.23 | β = 90 |
c = 51.23 | γ = 120 |
Symmetry | |
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Space Group | P 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | IMAGE PLATE | MARRESEARCH | 1995-12-21 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | 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 | 2.6 | 21 | 94.6 | 0.072 | 0.072 | 12 | 2.7 | 45363 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.6 | 2.64 | 96.2 | 0.286 | 3 | 1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1TTJ | 2.6 | 32 | 45363 | 2104 | 94.6 | 0.231 | 0.231 | 0.247 | RANDOM |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_angle_deg | 1.61 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na | |
x_angle_deg_prot | |
x_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10956 |
Nucleic Acid Atoms | |
Solvent Atoms | 53 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |