8QKS
Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.034
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3WAT | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.02 M Calcium chloride dihydrate 0.02 M Cadmium chloride hydrate 0.02 M Cobalt(II) chloride hexahydrate 20% w/v Polyethylene glycol 3,350 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.04 | 75.59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82.259 | α = 90 |
| b = 376.787 | β = 90.062 |
| c = 226.818 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 2 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 PILATUS3 6M | 2023-07-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9999 | Diamond | I24 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 3.99 | 65.604 | 99 | 0.993 | 0.319 | 6.8 | 115243 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 3.99 | 4.06 | 0.22 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.994 | 65.604 | 115176 | 1918 | 98.869 | 0.442 | 0.4413 | 0.4581 | RANDOM | 166.39 | |||||||
| 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] | |
| -0.609 | 4.384 | 2.822 | -2.222 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_lrange_it | 37.565 |
| r_dihedral_angle_3_deg | 17.905 |
| r_mcangle_it | 15.724 |
| r_scangle_it | 13.044 |
| r_dihedral_angle_6_deg | 12.355 |
| r_mcbond_it | 8.754 |
| r_dihedral_angle_2_deg | 8.6 |
| r_dihedral_angle_1_deg | 8.474 |
| r_scbond_it | 6.868 |
| r_angle_refined_deg | 1.711 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 32276 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
