2CE6
Structure of Helix Pomatia agglutinin with no ligands
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2CCV | PDB ENTRY 2CCV |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5). | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.53 | 44.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 61.6 | α = 90 |
| b = 61.6 | β = 90 |
| c = 105 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 2 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 | ADSC CCD | MIRROR | 2002-11-10 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
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 | 2.4 | 52.49 | 99.8 | 0.07 | 22.67 | 7.35 | 5042 | 56 | |||||||||||
| 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 | 2.4 | 2.43 | 99.8 | 0.38 | 2.59 | 4.37 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2CCV | 2.4 | 47.57 | 4785 | 236 | 99.6 | 0.224 | 0.222 | 0.22 | 0.266 | 0.28 | RANDOM | 52.99 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -2.02 | -1.01 | -2.02 | 3.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.573 |
| r_dihedral_angle_4_deg | 23.151 |
| r_dihedral_angle_3_deg | 15.467 |
| r_dihedral_angle_1_deg | 5.9 |
| r_scangle_it | 2.058 |
| r_angle_refined_deg | 1.458 |
| r_scbond_it | 1.335 |
| r_mcangle_it | 0.991 |
| r_mcbond_it | 0.804 |
| r_angle_other_deg | 0.787 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 780 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 25 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
