6GXE

Carbonic Anhydrase CAIX mimic in complex with inhibitor JS14


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8291Complex was prepared by adding 1-fold molar excess of inhibitor (dissolved in pure DMSO) to 25 mg/mL protein solution in water. 2 uL of complex solution were mixed with 1 uL of precipitant solution containing 1.6M sodium citrate, 50mM Tris H2SO4 pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.141.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.92α = 90
b = 41.22β = 103.89
c = 72.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300KVariMaxHF Arc)Sec2017-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5

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
11.339.5587.20.030.032127.835.0595150317.492
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)
11.31.3351.70.2090.2680.8883.852.533

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.339.5550472103187.250.125470.124890.15433RANDOM15.254
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]
-0.14-0.120.080.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg18.208
r_sphericity_free15.026
r_dihedral_angle_3_deg11.026
r_sphericity_bonded8.414
r_dihedral_angle_1_deg7.116
r_scangle_other2.622
r_long_range_B_refined2.621
r_long_range_B_other2.552
r_rigid_bond_restr2.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg18.208
r_sphericity_free15.026
r_dihedral_angle_3_deg11.026
r_sphericity_bonded8.414
r_dihedral_angle_1_deg7.116
r_scangle_other2.622
r_long_range_B_refined2.621
r_long_range_B_other2.552
r_rigid_bond_restr2.463
r_scbond_it2.154
r_scbond_other2.153
r_mcangle_it1.641
r_mcangle_other1.64
r_angle_refined_deg1.624
r_mcbond_it1.416
r_mcbond_other1.322
r_angle_other_deg1.087
r_chiral_restr0.089
r_gen_planes_other0.016
r_gen_planes_refined0.014
r_bond_refined_d0.01
r_bond_other_d0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2022
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction