4D5A
Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CI7 | PDB ENTRY 4CI7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 0.18 M NACL, 90 MM TRIS PH 8.0, 18% PEG 6000, 0.02% W/V 1,4-DIAMINOBUTANE, 0.02% W/V CYSTAMINE DIHYDROCHLORIDE, 0.02% W/V DILOXANIDE FUROATE, 0.02% W/V SARCOSINE, 0.02% W/V SPERMINE, 2MM SODIUM HEPES PH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.094 | α = 65.22 |
b = 70.152 | β = 89.89 |
c = 78.852 | γ = 80.18 |
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 | 2014-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 1.6 | 47.3 | 90.8 | 0.09 | 6.8 | 2.8 | 110175 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.6 | 1.63 | 49.9 | 0.47 | 2.1 | 2.5 |
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 | PDB ENTRY 4CI7 | 1.6 | 71.38 | 104911 | 5261 | 90.8 | 0.18252 | 0.18112 | 0.21055 | RANDOM | 15.346 |
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] | |
-1.33 | -0.17 | 0.15 | 1.46 | -0.53 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.291 |
r_dihedral_angle_4_deg | 15.069 |
r_dihedral_angle_3_deg | 12.45 |
r_dihedral_angle_1_deg | 6.073 |
r_mcangle_it | 1.552 |
r_angle_refined_deg | 1.274 |
r_scbond_it | 1.062 |
r_mcbond_it | 0.899 |
r_mcbond_other | 0.895 |
r_angle_other_deg | 0.734 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6350 |
Nucleic Acid Atoms | |
Solvent Atoms | 791 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
xia2 | data scaling |
PHASER | phasing |