2ZGC
Crystal Structure of Active Human Granzyme M
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 289 | 0.1M BICINE, 0.2M Li2SO4, 0.1M MGCL2, 19% PEG3350, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.46 | 64.45 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 74.391 | α = 90 |
| b = 74.391 | β = 90 |
| c = 113.199 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 93 | CCD | MAR CCD 165 mm | 2007-07-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BSRF BEAMLINE 3W1A | 1.000 | BSRF | 3W1A |
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 | 1.96 | 50 | 98.5 | 0.065 | 28 | 6.1 | 26720 | 26319 | 30 | ||||||||||
| 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 | 1.96 | 2.01 | 92.1 | 0.34 | 2.08 | 3.6 | 1596 | ||||||||||||
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 | PDB ENTRY 1DST | 1.96 | 32.56 | 24940 | 1327 | 98.66 | 0.21166 | 0.20925 | 0.25701 | RANDOM | 41.285 | ||||||
| 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] | |
| 0.03 | 0.02 | 0.03 | -0.05 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.58 |
| r_dihedral_angle_4_deg | 21.308 |
| r_dihedral_angle_3_deg | 15.701 |
| r_dihedral_angle_1_deg | 6.398 |
| r_scangle_it | 3.866 |
| r_scbond_it | 2.534 |
| r_angle_refined_deg | 1.726 |
| r_mcangle_it | 1.632 |
| r_mcbond_it | 1.083 |
| r_nbtor_refined | 0.305 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1748 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 282 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MAR345dtb | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
