2GNN
Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 0.6 M Ammonium sulfate, 3% PEG 4K, 0.1 M Sodium citrate, 0.3% Benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.10419 | 75.902153 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.6 | α = 90 |
b = 98.6 | β = 90 |
c = 240 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | MAR CCD 165 mm | 2004-07-27 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2004-07-31 | M | SINGLE WAVELENGTH | ||||||
1,2 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.00017 | SLS | X06SA |
2 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.698383 | SLS | X06SA |
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 | 2.3 | 48.48 | 93.4 | 0.081 | 14.58 | 52820 | 57.637 |
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 | 2.3 | 2.4 | 98.4 | 85.4 | 0.799 | 3.1 | 6199 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 2.3 | 48.48 | 52820 | 2687 | 98.66 | 0.224 | 0.224 | 0.223 | 0.247 | RANDOM | 66.047 |
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] | |
1.93 | 1.93 | -3.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.619 |
r_dihedral_angle_3_deg | 15.601 |
r_dihedral_angle_4_deg | 12.628 |
r_scangle_it | 7.725 |
r_scbond_it | 5.293 |
r_dihedral_angle_1_deg | 5.052 |
r_mcangle_it | 3.347 |
r_mcbond_it | 2.075 |
r_angle_refined_deg | 1.25 |
r_nbtor_refined | 0.293 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2831 |
Nucleic Acid Atoms | |
Solvent Atoms | 177 |
Heterogen Atoms | 132 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
SHELXD | phasing |