3WDC
N-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cyclomarin A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 291 | 0.2M ammonium acetate, 20% polyethylene glycol 3350, 0.025M magnesium, pH 7.5, VAPOR DIFFUSION, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.74 | 29.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.88 | α = 90 |
b = 58.69 | β = 90 |
c = 63.62 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 298 | PIXEL | PSI PILATUS 6M | 2011-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.18 | 45 | 42423 |
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 | 3WDB | 1.18 | 30 | 40221 | 2141 | 99.78 | 0.1241 | 0.1223 | 0.1594 | RANDOM | 13.093 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.09 | 0.01 | 0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 43.556 |
r_dihedral_angle_2_deg | 37.094 |
r_dihedral_angle_4_deg | 18.187 |
r_dihedral_angle_3_deg | 15.017 |
r_sphericity_bonded | 12.27 |
r_dihedral_angle_1_deg | 4.811 |
r_rigid_bond_restr | 3.811 |
r_angle_refined_deg | 1.985 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1217 |
Nucleic Acid Atoms | |
Solvent Atoms | 167 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |