4BSW
Heterodimeric Fc Antibody Azymetric Variant 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J6E | PDB ENTRY 2J6E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | VIA HANGING DROP VAPOR DIFFUSION METHOD AT A RATIO OF 2:1 OF 8.5 MG/ML OF AZYMETRIC VARIANT 2 ABOVE A MOTHER LIQUOR SOLUTION COMPOSED OF 5% (V/V) ETHYLENE GLYCOL, 18% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.15 M AMMONIUM IODIDE WITH AID OF MICROSEEDING. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.677 | α = 90 |
b = 74.715 | β = 90 |
c = 148.87 | 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 | MARRESEARCH MX300HE | COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) | 2012-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08B1-1 | CLSI | 08B1-1 |
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 | 2.1 | 47 | 99.9 | 0.07 | 15.9 | 6.8 | 33200 |
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 | 2.1 | 2.21 | 99.9 | 0.5 | 4 | 7 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 2J6E | 2.15 | 36.26 | 29307 | 1557 | 99.01 | 0.20296 | 0.19999 | 0.25937 | RANDOM | 45.511 |
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] | |
-2.3 | 0.94 | 1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.14 |
r_dihedral_angle_4_deg | 17.722 |
r_dihedral_angle_3_deg | 17.076 |
r_dihedral_angle_1_deg | 10.589 |
r_angle_refined_deg | 1.526 |
r_chiral_restr | 0.106 |
r_gen_planes_refined | 0.013 |
r_bond_refined_d | 0.01 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3458 |
Nucleic Acid Atoms | |
Solvent Atoms | 371 |
Heterogen Atoms | 243 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |