4S1D
Structure of IgG1 Fab fragment in complex with Biotincytidinamide
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 0.15M ammonium sulfate, 0.1M MES, 15%PEG 4000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 48.87 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 89.094 | α = 90 |
| b = 119.62 | β = 117.15 |
| c = 96.181 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | PIXEL | PSI PILATUS 6M | 2011-10-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1 | SLS | X10SA |
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 | 2.35 | 119 | 99.9 | 0.057 | 10.29 | 3.47 | 74713 | 74645 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.35 | 2.4 | 99.9 | 0.65 | 3.53 | 3658 | |||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | unpublished in house Fab fragment structure | 2.5 | 119 | 62797 | 58977 | 3132 | 99.91 | 0.22799 | 0.22547 | 0.27446 | RANDOM | 78.96 | |||||
| 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] | |
| -1.24 | 4.17 | -2.72 | -0.21 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.185 |
| r_dihedral_angle_4_deg | 14.784 |
| r_dihedral_angle_3_deg | 13.842 |
| r_dihedral_angle_1_deg | 5.638 |
| r_long_range_B_refined | 5.383 |
| r_long_range_B_other | 5.342 |
| r_mcangle_it | 1.929 |
| r_mcangle_other | 1.929 |
| r_scangle_other | 1.555 |
| r_mcbond_it | 1.109 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13109 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 336 |
| Heterogen Atoms | 105 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DA+ | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SADABS | data scaling |
