4INP
The crystal structure of Helicobacter pylori Ceue (HP1561) with Ni(II) bound
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 8 | 293 | 0.1 M SPG buffer, 25% w/v PEG1500, pH 8.0, VAPOR DIFFUSION, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.24 | 45.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.18 | α = 90 |
| b = 76.95 | β = 94.52 |
| c = 72.78 | 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 | CCD | ADSC QUANTUM 315r | 2011-06-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 | |
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 | 2.3 | 52.79 | 92 | 0.078 | 8.8 | 2.5 | 27148 | ||||||||||||
| 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 | 2.3 | 2.42 | 96.2 | 0.226 | 5.2 | 2.5 | |||||||||||||
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 3UI8 | 2.3 | 52.79 | 25743 | 1370 | 91.7 | 0.193 | 0.189 | 0.268 | RANDOM | 22.24 | ||||||
| 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] | |
| 0.15 | 0.2 | -0.08 | -0.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.889 |
| r_dihedral_angle_3_deg | 18.866 |
| r_dihedral_angle_4_deg | 16.44 |
| r_dihedral_angle_1_deg | 6.639 |
| r_scangle_it | 4.724 |
| r_scbond_it | 2.846 |
| r_mcangle_it | 1.828 |
| r_angle_refined_deg | 1.74 |
| r_mcbond_it | 0.989 |
| r_chiral_restr | 0.127 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4758 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 200 |
| Heterogen Atoms | 38 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
