5GUI
Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpC1 from Arabidopsis thaliana
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WDC |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 293 | 0.1M SODIUM CITRATE DEHYDRATE, 1.0M AMMONIUM PHOSPHATE MONOBASIC |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.1 | α = 90 |
b = 44.29 | β = 90 |
c = 97.56 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 103 | CCD | MARMOSAIC 225 mm CCD | 2015-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | RRCAT INDUS-2 BEAMLINE PX-BL21 | 0.9794 | RRCAT INDUS-2 | PX-BL21 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.2 | 17.54 | 97.9 | 0.067 | 9.4 | 4.8 | 54126 | 11.9 |
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) | |||||||||||
1 | 1.2 | 1.26 | 98.4 | 0.565 | 2.5 | 4.7 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3WDC | 1.2 | 17.54 | 51310 | 2742 | 97.9 | 0.147 | 0.167 | RANDOM | 18 |
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] | |
-1.84 | 0.5 | 1.34 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 34.721 |
r_dihedral_angle_2_deg | 29.94 |
r_dihedral_angle_4_deg | 17.249 |
r_sphericity_bonded | 16.688 |
r_dihedral_angle_3_deg | 12.895 |
r_dihedral_angle_1_deg | 5.202 |
r_long_range_B_refined | 4.138 |
r_long_range_B_other | 3.934 |
r_scangle_other | 3.885 |
r_scbond_other | 3.262 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1141 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
Aimless | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |