6Z04

Nido-carborane butyl-sulfonamide in complex with CA IX mimic


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OGP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29150 mM Tris pH=7.8 1.6 M Natrium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.141.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.035α = 90
b = 41.345β = 103.98
c = 72.682γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-21MSINGLE 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
11.0540.7997.80.0690.0820.9977.93.25811143313.945
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)
11.051.1194.60.8351.010.4671.123.081

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 SYNTHESISTHROUGHOUT5OGP1.0540.79109331210197.860.14120.14080.1578RANDOM15.626
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]
-0.13-0.03-0.090.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.733
r_dihedral_angle_4_deg18.118
r_sphericity_free13.778
r_dihedral_angle_3_deg10.535
r_dihedral_angle_1_deg6.997
r_sphericity_bonded6.77
r_angle_other_deg2.394
r_rigid_bond_restr2.284
r_angle_refined_deg1.629
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.733
r_dihedral_angle_4_deg18.118
r_sphericity_free13.778
r_dihedral_angle_3_deg10.535
r_dihedral_angle_1_deg6.997
r_sphericity_bonded6.77
r_angle_other_deg2.394
r_rigid_bond_restr2.284
r_angle_refined_deg1.629
r_chiral_restr0.107
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2010
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms20

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
FFTphasing