Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1YV5 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.5M NaCl, 0.1M acetate buffer |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.78 | 55.73 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 111.966 | α = 90 |
| b = 111.966 | β = 90 |
| c = 72.754 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 41 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | CCD | ADSC QUANTUM 270 | | 2013-11-17 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | OSCILLATION CAMERA | CUSTOM-MADE | | 2013-11-06 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1 | Photon Factory | AR-NW12A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 3.99 | JPARC MLF | BL-03 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.4 | 50.07 | 96.2 | 0.062 | | | | | | | 7.1 | | 87200 | | | |
| 2 | 2.4 | 53.57 | 96.2 | 0.107 | | | | | | | 3.8 | | 18415 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.4 | 1.42 | | 0.482 | | | | | | | 3.2 | |
| 2 | 2.4 | 2.49 | | 0.612 | | | | | | | 2.7 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | 1.402 | 50.07 | | | 87160 | 87160 | 4389 | 96.22 | | 0.1948 | 0.1936 | 0.19 | 0.2183 | 0.23 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.4 | 53.57 | | | 18386 | 18386 | 902 | 98.47 | | 0.1878 | 0.1857 | | 0.2292 | | | |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 18.782 |
| f_angle_d | 0.919 |
| f_chiral_restr | 0.139 |
| f_bond_d | 0.006 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2765 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 106 |
| Heterogen Atoms | 20 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| HKL-2000 | data collection |
