3WC7
Carboxypeptidase B in complex with EF6265
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WAB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 296 | 100mM sodium cacodylate (pH 5.3-6.8), 100mM zinc acetate, 5-15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.36 | α = 90 |
b = 79.36 | β = 90 |
c = 100.16 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | ADSC QUANTUM 4 | 2009-12-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 0.978 | Photon Factory | BL-6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 62.202 | 100 | 0.088 | 25.9 | 13.6 | 25909 | 25909 |
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) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 2 | 100 | 0.336 | 0.336 | 0.349 | 0.095 | 2.1 | 13.5 | 3705 |
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 | 3WAB | 1.9 | 27.02 | 25832 | 1287 | 99.92 | 0.1824 | 0.1812 | 0.2071 | RANDOM | 30.8698 |
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] | |
0.07 | 0.07 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.843 |
r_dihedral_angle_4_deg | 13.798 |
r_dihedral_angle_3_deg | 13.053 |
r_dihedral_angle_1_deg | 6.464 |
r_scangle_it | 2.167 |
r_scbond_it | 1.9 |
r_angle_refined_deg | 1.825 |
r_rigid_bond_restr | 1.259 |
r_mcangle_it | 1.039 |
r_mcbond_it | 0.844 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2436 |
Nucleic Acid Atoms | |
Solvent Atoms | 325 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
MOSFLM | data reduction |
PHASER | phasing |