3V95
Crystal structure of monoclonal human anti-rhesus D Fc and IgG1 t125(yb2/0) in the presence of EDTA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3V8C | PDB ENTRY 3V8C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.1 | 293 | 12.8% MPEG 5000, 21.5% ETHYLENE GLYCOL, 0.002M EDTA, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.38 | α = 90 |
b = 79.12 | β = 90 |
c = 138.91 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC QUANTUM 210 | MIRRORS | 2004-11-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.7 | 50 | 99.4 | 0.09 | 0.1 | 17.56 | 7.8 | 15731 | -3 | 44.07 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.69 | 2.85 | 97.2 | 0.538 | 0.491 | 3.78 | 7.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 3V8C | 2.7 | 41.89 | 15731 | 14943 | 787 | 100 | 0.255 | 0.251 | 0.321 | RANDOM | 39.73 |
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] | |
-1.62 | 0.19 | 1.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.681 |
r_dihedral_angle_3_deg | 22.281 |
r_dihedral_angle_4_deg | 22.166 |
r_dihedral_angle_1_deg | 7.437 |
r_scangle_it | 2.653 |
r_angle_refined_deg | 1.795 |
r_scbond_it | 1.565 |
r_mcangle_it | 1.401 |
r_mcbond_it | 0.753 |
r_chiral_restr | 0.106 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3356 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 212 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |