5FVN
X-ray crystal structure of Enterobacter cloacae OmpE36 porin.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2J1N | PDB ENTRY 2J1N |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | 0.4M AMMONIUM SULFATE, 0.1M MES, 10% W/V PEG 3350, PH6.5 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.6 | 65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 109.749 | α = 90 |
| b = 123.26 | β = 91.01 |
| c = 116.01 | 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 | 100 | PIXEL | DECTRIS PIXEL | 2014-11-24 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 | |
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 | 1.45 | 48.92 | 100 | 0.08 | 8 | 3.7 | 529555 | -3 | |||||||||||
| 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 | 1.45 | 1.47 | 100 | 0.05 | 1.6 | 3.7 | |||||||||||||
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 2J1N | 1.45 | 115.99 | 529555 | 13912 | 99.96 | 0.15613 | 0.15543 | 0.17 | 0.18308 | 0.19 | RANDOM | 18.211 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.23 | -1.16 | -1.03 | 0.84 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.018 |
| r_sphericity_free | 34.861 |
| r_sphericity_bonded | 19.221 |
| r_dihedral_angle_4_deg | 17.019 |
| r_dihedral_angle_3_deg | 11.087 |
| r_dihedral_angle_1_deg | 6.578 |
| r_scbond_it | 4.095 |
| r_mcangle_it | 3.044 |
| r_rigid_bond_restr | 2.71 |
| r_mcbond_it | 2.562 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 16092 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1910 |
| Heterogen Atoms | 1513 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
