2OAY
Crystal structure of latent human C1-inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CAA | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1QMB | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1E05 | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1DVM | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1C8O | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1JTI | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1JJO | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1MTP | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1HLE | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
experimental model | PDB | 1JRR | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.85 M NaH2PO4, 0.85 M KH2PO4, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.903 | α = 90 |
b = 98.903 | β = 90 |
c = 94.684 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | MAR CCD 165 mm | mirrors | 2006-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.8162 | EMBL/DESY, HAMBURG | X11 |
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 | 2.35 | 84.52 | 99.8 | 0.097 | 20.29 | 14.6 | 21930 | -3 | 32.4 |
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 | 2.35 | 2.4 | 100 | 0.652 | 3.89 | 9.54 | 1341 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR | 2.35 | 84.52 | 20803 | 20803 | 1125 | 99.83 | 0.17595 | 0.17595 | 0.17363 | 0.21794 | RANDOM | 32.433 |
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] | |
0.29 | 0.14 | 0.29 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 7.479 |
r_scangle_it | 3.367 |
r_mcangle_it | 3.238 |
r_scbond_it | 2.123 |
r_mcbond_it | 2.07 |
r_angle_refined_deg | 1.764 |
r_angle_other_deg | 0.804 |
r_symmetry_vdw_other | 0.39 |
r_symmetry_vdw_refined | 0.273 |
r_nbd_other | 0.256 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2845 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |