Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5YFJ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.7 M NaCl, 3% PEG 6000, 25% MPD, 0.1% Low Melting Agarose | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.25 | 62.23 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.14 | α = 90 |
| b = 98.14 | β = 90 |
| c = 255.681 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 1 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HF | 2016-12-03 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.75 | 85.23 | 100 | 0.154 | 0.165 | 0.058 | 0.995 | 12 | 7.9 | 37157 | |||||||||
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 | 5YFJ | 2.75 | 85.23 | 35206 | 1890 | 100 | 0.1555 | 0.1519 | 0.16 | 0.224 | 0.22 | RANDOM | 36.164 | ||||
| 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] | |
| 0.99 | 0.5 | 0.99 | -3.21 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.681 |
| r_dihedral_angle_4_deg | 20.761 |
| r_dihedral_angle_3_deg | 17.757 |
| r_dihedral_angle_1_deg | 6.489 |
| r_angle_refined_deg | 1.744 |
| r_angle_other_deg | 1.004 |
| r_chiral_restr | 0.089 |
| r_bond_refined_d | 0.013 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7638 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 254 |
| Heterogen Atoms | 134 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data collection |
| MOSFLM | data processing |
| Aimless | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| Coot | model building |
| PDB_EXTRACT | data extraction |
