9R8X | pdb_00009r8x

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
3.4364.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.491α = 90
b = 152.491β = 90
c = 172.422γ = 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 14.10.918400BESSY14.1

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
1247.951000.08421.110.410101228.03
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)
122.031001.2082.310.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT247.9594661536299.010.175430.173450.18320.210210.2138RANDOM31.887
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]
0.440.220.44-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.469
r_long_range_B_refined8.071
r_long_range_B_other8.02
r_dihedral_angle_2_deg7.81
r_scangle_other6.573
r_dihedral_angle_1_deg6.376
r_mcangle_it4.718
r_mcangle_other4.718
r_scbond_it4.461
r_scbond_other4.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.469
r_long_range_B_refined8.071
r_long_range_B_other8.02
r_dihedral_angle_2_deg7.81
r_scangle_other6.573
r_dihedral_angle_1_deg6.376
r_mcangle_it4.718
r_mcangle_other4.718
r_scbond_it4.461
r_scbond_other4.46
r_mcbond_it3.434
r_mcbond_other3.433
r_angle_refined_deg1.788
r_angle_other_deg0.595
r_chiral_restr0.089
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms7388
Nucleic Acid Atoms
Solvent Atoms707
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing