3EIM
Metal exchange in Thermolysin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TMN | PDB ENTRY 1TMN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 288 | 50mM Tris/HCl, 50%DMSO, 1,9MCsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 47.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.71 | α = 90 |
b = 92.71 | β = 90 |
c = 128.65 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | Double crystal Si[111] monochromator | 2007-11-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | 1.000 | EMBL/DESY, HAMBURG | X12 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.88 | 30 | 99.9 | 0.106 | 18.3 | 7.3 | 27294 | 27294 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.88 | 1.91 | 0.461 | 4.3 | 7.5 | 1347 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R | PDB ENTRY 1TMN | 1.88 | 10 | 27030 | 27030 | 1356 | 100 | 0.1856 | 0.1856 | 0.1856 | 0.2523 | 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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
3 | 2632.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.051 |
s_non_zero_chiral_vol | 0.038 |
s_zero_chiral_vol | 0.032 |
s_from_restr_planes | 0.0237 |
s_angle_d | 0.021 |
s_anti_bump_dis_restr | 0.009 |
s_bond_d | 0.006 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2413 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |