5I1E
CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-53/IGKV1-39
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 16% PEG 3K, 0.2 M AMMONIUM SULFATE, 5% DIOXANE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.38 | α = 90 |
b = 89.38 | β = 90 |
c = 212.38 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 | 95 | CCD | RIGAKU SATURN 944 | VARIMAX HF | 2009-09-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 2.7 | 30 | 99.6 | 0.095 | 38.3 | 20.6 | 14402 | -3 | 33.2 |
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 | 2.7 | 2.77 | 96.8 | 0.451 | 8.1 | 19.3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.7 | 15 | 13583 | 722 | 94.6 | 0.19455 | 0.19089 | 0.26362 | RANDOM | 49.1 |
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] | |
0.37 | 0.19 | 0.37 | -0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scbond_it | 40.751 |
r_scangle_it | 40.34 |
r_dihedral_angle_2_deg | 35.847 |
r_dihedral_angle_4_deg | 19.178 |
r_dihedral_angle_3_deg | 16.616 |
r_dihedral_angle_1_deg | 6.346 |
r_mcangle_it | 4.735 |
r_mcbond_it | 2.307 |
r_angle_refined_deg | 1.213 |
r_chiral_restr | 0.073 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3236 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
REFMAC | refinement |
REFMAC | phasing |