Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1DFN | Based on monomer of HNP-3 (PDB ID code 1DFN) |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | tri-sodium citrate dihydrate, Tris/HCl, PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.07 | 40.65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.148 | α = 90 |
| b = 47.148 | β = 90 |
| c = 50.643 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 42 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2004-06-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-BM | 0.9200 | APS | 22-BM |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.1 | 30 | 97.7 | 0.07 | 15.7 | 10.2 | 24405 | 24405 | |||||||||||
| 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 | 1.1 | 1.15 | 89.8 | 0.429 | 2.2 | 3.9 | |||||||||||||
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 (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Based on monomer of HNP-3 (PDB ID code 1DFN) | 1.3 | 19.47 | 13688 | 734 | 98.76 | 0.16116 | 0.16116 | 0.16033 | 0.19 | 0.17676 | RANDOM | 15.779 | ||||
| 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 | 0.03 | -0.06 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 19.488 |
| r_dihedral_angle_3_deg | 10.723 |
| r_dihedral_angle_4_deg | 10.136 |
| r_sphericity_free | 9.842 |
| r_dihedral_angle_1_deg | 8.149 |
| r_angle_other_deg | 3.881 |
| r_sphericity_bonded | 3.526 |
| r_scangle_it | 3.38 |
| r_mcangle_it | 3.102 |
| r_scbond_it | 3.017 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 468 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 75 |
| Heterogen Atoms | 8 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MAR345 | data collection |
| SCALEPACK | data scaling |
| AMoRE | phasing |
