Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 1YV5 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.5M NaCl, 0.1M acetate buffer |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.78 | 55.73 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 111.966 | α = 90 |
b = 111.966 | β = 90 |
c = 72.754 | γ = 90 |
Symmetry |
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Space Group | P 41 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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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 |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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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 |
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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 |
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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 |
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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) |
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1 | 1.4 | 1.42 | | 0.482 | | | | | | | 3.2 | |
2 | 2.4 | 2.49 | | 0.612 | | | | | | | 2.7 | |
Refinement
Statistics |
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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 | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.402 | 50.07 | | | 87160 | 87160 | 4389 | 96.22 | | 0.1948 | 0.1936 | 0.2183 | | |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.4 | 53.57 | | | 18386 | 18386 | 902 | 98.47 | | 0.1878 | 0.1857 | 0.2292 | | |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2765 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 20 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
HKL-2000 | data collection |