4M7K
Crystal structure of anti-tissue factor antibody 10H10
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1 M cacodylate, pH 6.5, 24% PEG8000, 1 M sodium acetate, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.77 | α = 90 |
b = 135.51 | β = 90 |
c = 88.25 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2007-09-11 | 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 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.9 | 30 | 99.4 | 0.06 | 26.3 | 9.5 | 38664 | 38664 | -3 | 27.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.9 | 1.95 | 95.3 | 0.365 | 4.2 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRIES 1VGE, 1MVU, AND 1D5I | 1.9 | 15 | 37585 | 37585 | 997 | 99.4 | 0.2058 | 0.2058 | 0.20479 | 0.24276 | RANDOM | 32.9 |
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] | |
0.58 | -0.77 | 0.19 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.257 |
r_scangle_it | 23.101 |
r_scbond_it | 21.428 |
r_dihedral_angle_4_deg | 12.781 |
r_dihedral_angle_3_deg | 12.134 |
r_dihedral_angle_1_deg | 5.973 |
r_mcangle_it | 4.263 |
r_mcbond_it | 2.577 |
r_angle_refined_deg | 1.059 |
r_chiral_restr | 0.067 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3402 |
Nucleic Acid Atoms | |
Solvent Atoms | 347 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
AMoRE | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |