5HMM
Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EXN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 280 | PACT H2: 0.2M Na bromide, 0.1M Bis Tris propane pH 8.5, 20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.831 | α = 66.88 |
b = 58.591 | β = 79.4 |
c = 59.729 | γ = 73.78 |
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 | PIXEL | DECTRIS PILATUS 6M | 2011-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97836 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.5 | 54.735 | 93.1 | 0.083 | 0.093 | 0.042 | 10.5 | 3.8 | 83343 | 83343 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.5 | 1.58 | 90.4 | 0.322 | 0.322 | 0.296 | 1.6 | 2.2 | 11812 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1EXN | 1.5 | 38.35 | 79049 | 4123 | 92.77 | 0.1501 | 0.1477 | 0.1967 | RANDOM | 19.387 |
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] | |
0.28 | 0.37 | 0.58 | 0.12 | -0.21 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 33.009 |
r_dihedral_angle_2_deg | 32.03 |
r_sphericity_bonded | 27.767 |
r_dihedral_angle_4_deg | 13.935 |
r_rigid_bond_restr | 11.794 |
r_dihedral_angle_3_deg | 11.609 |
r_dihedral_angle_1_deg | 5.294 |
r_mcangle_it | 3.066 |
r_mcbond_it | 2.778 |
r_mcbond_other | 2.729 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4349 |
Nucleic Acid Atoms | |
Solvent Atoms | 598 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
PHASER | phasing |