6EBE

Bioreductive 4-hydroxy-3-nitro-5-ureido-benzenesulfonamides selectively target the tumor-associated carbonic anhydrase isoforms IX and XII and show hypoxia-enhanced cytotoxicity against human cancer cell lines.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 298.0
Details 1.6 M Sodium citrate, 50 mM Tris-HCl, pH 7.8

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.86 α = 90
b = 41.81 β = 104.56
c = 72.91 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2017-07-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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
1.88 50 88.9 0.095 -- -- 2.4 -- 18329 -- -- 20.74
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.88 1.91 90.8 0.592 -- -- 2.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.88 32.383 -- 1.35 -- 18182 900 88.22 -- 0.171 0.1682 0.2277 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.8795 1.9972 -- 153 2784 0.2222 0.2948 0.0 86.0
X Ray Diffraction 1.9972 2.1514 -- 150 2931 0.1928 0.2695 0.0 91.0
X Ray Diffraction 2.1514 2.3679 -- 155 2944 0.1796 0.2392 0.0 91.0
X Ray Diffraction 2.3679 2.7103 -- 149 2944 0.1885 0.2472 0.0 90.0
X Ray Diffraction 2.7103 3.4142 -- 149 2888 0.1729 0.2208 0.0 88.0
X Ray Diffraction 3.4142 32.3883 -- 144 2791 0.1335 0.1911 0.0 83.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.9742
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.475
f_angle_d 1.295
f_bond_d 0.009
f_chiral_restr 0.08
f_plane_restr 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 41

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10pre_2097
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.24
HKL-2000 data reduction
PHENIX phasing