8CO0

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5294CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
3.4664.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.951α = 90
b = 152.951β = 90
c = 172.438γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.97776MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.329.9399.50.1158.95.966667
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3694.10.8341.55.5

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 REPLACEMENTTHROUGHOUT2.329.9363380342799.940.163070.160440.21231RANDOM41.648
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]
0.50.250.5-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.493
r_dihedral_angle_3_deg15.193
r_long_range_B_other7.952
r_long_range_B_refined7.948
r_dihedral_angle_1_deg6.891
r_scangle_other6.191
r_mcangle_it4.867
r_mcangle_other4.867
r_scbond_it4.192
r_scbond_other4.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.493
r_dihedral_angle_3_deg15.193
r_long_range_B_other7.952
r_long_range_B_refined7.948
r_dihedral_angle_1_deg6.891
r_scangle_other6.191
r_mcangle_it4.867
r_mcangle_other4.867
r_scbond_it4.192
r_scbond_other4.191
r_mcbond_it3.369
r_mcbond_other3.369
r_angle_refined_deg1.715
r_angle_other_deg0.48
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7910
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement