5O0Z
Structure of laspartomycin C in complex with geranyl-phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293.15 | 20 mM CaCl2 and 37.5% v/v MPD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.05 | 59.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.933 | α = 90 |
b = 56.933 | β = 90 |
c = 56.933 | γ = 90 |
Symmetry | |
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Space Group | P 43 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M-F | 2016-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.28 | 28.47 | 100 | 0.067 | 0.032 | 0.994 | 15 | 9.4 | 8650 |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 1.28 | 40.26 | 8170 | 435 | 99.97 | 0.14605 | 0.14503 | 0.15 | 0.16506 | 0.17 | RANDOM | 20.443 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 33.601 |
r_dihedral_angle_2_deg | 28.217 |
r_sphericity_bonded | 13.599 |
r_dihedral_angle_3_deg | 12.178 |
r_dihedral_angle_1_deg | 5.499 |
r_scangle_other | 5.155 |
r_scbond_it | 4.626 |
r_scbond_other | 4.602 |
r_long_range_B_refined | 3.442 |
r_long_range_B_other | 3.4 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 156 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
Aimless | data scaling |
SHELXCD | phasing |