6FAX
Complex of Human CD40 Ectodomain with Lob 7.4 Fab
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | NA | |
2 | VAPOR DIFFUSION, HANGING DROP | 293 | NA |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.86 |
2.27 | 45.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 158.753 | α = 90 |
b = 158.753 | β = 90 |
c = 93.622 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-04-04 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2015-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.976254 | ESRF | ID23-1 |
2 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.969995 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.99 | 52 | 99.9 | 0.161 | 0.998 | 13.7 | 13.7 | 27589 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.99 | 3.18 | 99.3 | 0.912 | 2.4 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1U6A | 2.99 | 137.48 | 26355 | 1319 | 99.67 | 0.18707 | 0.18482 | 0.23121 | RANDOM | 84.715 |
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] | |
2.59 | 1.3 | 2.59 | -8.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.454 |
r_dihedral_angle_3_deg | 20.7 |
r_dihedral_angle_4_deg | 18.582 |
r_long_range_B_refined | 14.058 |
r_long_range_B_other | 14.057 |
r_scangle_other | 11.561 |
r_dihedral_angle_1_deg | 10.747 |
r_mcangle_it | 10.217 |
r_mcangle_other | 10.215 |
r_scbond_it | 8.25 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4057 |
Nucleic Acid Atoms | |
Solvent Atoms | 21 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |