3IWW
Crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DBIBzL, a urea-based inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 33% v/v pentaerythritol propoxylate PO/OH 5/4, 1.5 % w/v PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 62.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.068 | α = 90 |
b = 130.035 | β = 90 |
c = 157.951 | 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 | MARMOSAIC 300 mm CCD | high-resolution Rosenbaum-Rock monochromator for sagital focusing, Rosenbaum-Rock vertical focusing mirror | 2008-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | 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 | 2.15 | 20 | 99.8 | 0.125 | 16 | 5.6 | 56427 | 56427 | -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 | 2.15 | 2.23 | 98.5 | 0.447 | 3.2 | 3.9 | 5526 |
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 | 2.3 | 20 | 44049 | 1420 | 97.93 | 0.16621 | 0.16489 | 0.20581 | RANDOM | 23.613 |
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] | |
2.46 | -3.22 | 0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.871 |
r_dihedral_angle_3_deg | 16.62 |
r_dihedral_angle_4_deg | 16.437 |
r_dihedral_angle_1_deg | 6.233 |
r_scangle_it | 5.079 |
r_scbond_it | 3.097 |
r_angle_refined_deg | 1.822 |
r_mcangle_it | 1.735 |
r_mcbond_it | 0.927 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5529 |
Nucleic Acid Atoms | |
Solvent Atoms | 233 |
Heterogen Atoms | 209 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
REFMAC | phasing |