6YZM

Carborane nido-pentyl-sulfonamide in complex with CA IX mimic


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GXE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82911.6 M sodium citrate, 50 mM Tris-H2SO4
Crystal Properties
Matthews coefficientSolvent content
2.0239.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.666α = 90
b = 41.001β = 103.65
c = 71.212γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.539.2198.80.0490.0590.99913.43.3073724625.656
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
11.51.5998.20.640.7710.7351.713.157

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6GXE1.539.2135381186398.850.16450.16290.1945RANDOM21.415
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]
-1.33-0.55-0.692.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_4_deg19.812
r_dihedral_angle_3_deg12.173
r_dihedral_angle_1_deg6.671
r_angle_refined_deg1.725
r_angle_other_deg1.641
r_chiral_restr0.108
r_bond_refined_d0.015
r_bond_other_d0.012
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_4_deg19.812
r_dihedral_angle_3_deg12.173
r_dihedral_angle_1_deg6.671
r_angle_refined_deg1.725
r_angle_other_deg1.641
r_chiral_restr0.108
r_bond_refined_d0.015
r_bond_other_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2022
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms21

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
FFTphasing