6NMV
Non-Blocking Fab 218 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 285 | 0.1 M Tris-HCl, 0.2 M MgCl2, 25% w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.29 | α = 90 |
b = 76.09 | β = 95.26 |
c = 72.81 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2017-09-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | .97923 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.61 | 38.16 | 98.3 | 7.5 | 3.2 | 45887 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.61 | 2.68 | 97.7 | 0.7 | 3.3 |
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 | THROUGHOUT | 2.61 | 38.16 | 13589 | 880 | 98.19 | 0.2009 | 0.1945 | 0.3007 | RANDOM | 65.411 |
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] | |
0.86 | -1.16 | -3.23 | 2.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.135 |
r_dihedral_angle_3_deg | 19.002 |
r_dihedral_angle_4_deg | 15.44 |
r_dihedral_angle_1_deg | 9.493 |
r_angle_refined_deg | 1.479 |
r_angle_other_deg | 0.862 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3939 |
Nucleic Acid Atoms | |
Solvent Atoms | 20 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data scaling |
PHASER | phasing |