2XEF
Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P8
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OOT | PDB ENTRY 2OOT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 33% (V/V) PENTAERYTHRITOL PROPOXYLATE PO/OH 5/4, 1% (W/V) PEG 3350, 100 MM TRIS-HCL, pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.844 | α = 90 |
b = 130.026 | β = 90 |
c = 158.741 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | MARRESEARCH MX-300 | 2009-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
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 | 1.59 | 30 | 96.9 | 0.08 | 15.4 | 6.6 | 137748 | -3 |
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 | 1.59 | 1.65 | 77.9 | 0.44 | 2.6 | 2.6 |
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 2OOT | 1.59 | 30 | 135631 | 2037 | 96.92 | 0.16107 | 0.16075 | 0.18266 | RANDOM | 26.229 |
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] | |
0.62 | -1.84 | 1.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.534 |
r_dihedral_angle_3_deg | 13.41 |
r_dihedral_angle_4_deg | 13.027 |
r_dihedral_angle_1_deg | 5.6 |
r_scangle_it | 4.198 |
r_scbond_it | 2.598 |
r_angle_refined_deg | 1.692 |
r_mcangle_it | 1.638 |
r_mcbond_it | 0.985 |
r_chiral_restr | 0.124 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5524 |
Nucleic Acid Atoms | |
Solvent Atoms | 581 |
Heterogen Atoms | 244 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |