9R8Y | pdb_00009r8y

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 9FLF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52941.0 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)
Crystal Properties
Matthews coefficientSolvent content
3.4364.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.921α = 90
b = 151.921β = 90
c = 173.682γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2024-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91840BESSY14.1

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
11.9547.811000.2187.110.410892722.404
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)
11.951.981001.2981.59.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9547.8199209548496.090.214960.212840.22110.253570.2584RANDOM30.692
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]
0.460.230.46-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.436
r_dihedral_angle_2_deg9.476
r_long_range_B_refined7.638
r_long_range_B_other7.585
r_dihedral_angle_1_deg6.973
r_scangle_other5.542
r_mcangle_it4.514
r_mcangle_other4.514
r_scbond_it3.619
r_scbond_other3.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.436
r_dihedral_angle_2_deg9.476
r_long_range_B_refined7.638
r_long_range_B_other7.585
r_dihedral_angle_1_deg6.973
r_scangle_other5.542
r_mcangle_it4.514
r_mcangle_other4.514
r_scbond_it3.619
r_scbond_other3.619
r_mcbond_it3.089
r_mcbond_other3.088
r_angle_refined_deg1.72
r_angle_other_deg0.568
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms7381
Nucleic Acid Atoms
Solvent Atoms691
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing