3FRP
Crystal Structure of Cobra Venom Factor, a Co-factor for C3- and C5 convertase CVFBb
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A74 | PDB ENTRY 2A74 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 293 | 13% PEG 3350, 10 mM MES pH 6.8, 5 mM CaCl2, 200 mM NH4Cl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 134.138 | α = 90 |
b = 151.141 | β = 90 |
c = 76.787 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | CCD | MARMOSAIC 225 mm CCD | 2008-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
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 | 2.6 | 50 | 91.9 | 0.08 | 21.7 | 7.1 | 43934 |
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) | |||||||||||
2.6 | 2.69 | 73.9 | 0.31 | 2 | 2.1 |
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 2A74 | 2.61 | 50 | 41713 | 2221 | 91.16 | 0.25053 | 0.24799 | 0.29708 | RANDOM | 57.463 |
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] | |
1.84 | -0.41 | -1.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.228 |
r_dihedral_angle_3_deg | 18.299 |
r_dihedral_angle_4_deg | 17.327 |
r_dihedral_angle_1_deg | 6.251 |
r_scangle_it | 2.237 |
r_angle_refined_deg | 1.323 |
r_scbond_it | 1.318 |
r_mcangle_it | 1.016 |
r_mcbond_it | 0.536 |
r_chiral_restr | 0.084 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9076 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |