1U10
MEPA, active form with ZN in P1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TZP | MepA in the P21 form (1TZP) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | ammonium sulfate, MES, PEG monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.613 | α = 93.15 |
b = 77.988 | β = 95.93 |
c = 127.663 | γ = 90.75 |
Symmetry | |
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Space Group | P 1 |
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 | MARRESEARCH | 2004-04-27 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 0.9791, 0.9793, 1.2810 | MPG/DESY, HAMBURG | BW6 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.4 | 20 | 97.1 | 0.039 | 0.039 | 14.1 | 1.9 | 103423 | 103423 | 36 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.4 | 2.44 | 93.5 | 0.151 | 0.151 | 4 | 1.8 | 4917 |
Refinement
Statistics | |||||||||||||||||||
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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 | MAD combined with MR | THROUGHOUT | MepA in the P21 form (1TZP) | 2.4 | 20 | 49711 | 49711 | 2658 | 98.17 | 0.23551 | 0.23551 | 0.23393 | 0.2658 | RANDOM | 24.954 |
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] | |
1.34 | 0.31 | -0.09 | -0.15 | -0.68 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 3.669 |
r_angle_other_deg | 3.527 |
r_mcangle_it | 2.625 |
r_scbond_it | 2.549 |
r_mcbond_it | 1.688 |
r_angle_refined_deg | 1.615 |
r_dihedral_angle_1_deg | 1.531 |
r_symmetry_vdw_other | 0.361 |
r_symmetry_hbond_refined | 0.313 |
r_nbd_other | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11217 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MLPHARE | phasing |