6YOL
Meta-Nidocarborane propyl-sulfonamide in complex with CA IX mimic
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5OGP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 291 | 1.6 M sodium citrate, 50 mM Tris-H2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.032 | α = 90 |
b = 41.443 | β = 103.86 |
c = 72.703 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 6M | 2017-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.14 | 35.74 | 94.4 | 0.058 | 0.068 | 0.998 | 9.74 | 3.687 | 82863 | 18.22 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.14 | 1.21 | 83.8 | 1.022 | 1.202 | 0.493 | 1 | 3.497 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 5OGP | 1.15 | 35.74 | 80691 | 2098 | 94.94 | 0.1417 | 0.1409 | 0.1705 | RANDOM | 18.945 |
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] | |
-0.76 | 0.68 | -0.2 | 0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.795 |
r_sphericity_free | 22.688 |
r_dihedral_angle_4_deg | 17.685 |
r_dihedral_angle_3_deg | 11.42 |
r_sphericity_bonded | 10.851 |
r_dihedral_angle_1_deg | 6.703 |
r_rigid_bond_restr | 3.338 |
r_angle_refined_deg | 1.64 |
r_angle_other_deg | 1.374 |
r_chiral_restr | 0.102 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2009 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
FFT | phasing |