9FLF

Three-Dimensional Structure of Human Carbonic Anhydrase IX in Complex with a Covalent Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8Q18 

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, 2-5 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
3.6566.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.11α = 90
b = 152.11β = 90
c = 172.51γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2024-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

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
12.252.351000.07217.210.77552849.468
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)
12.22.251001.1591.911

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 REPLACEMENTTHROUGHOUT2.252.3571653387499.990.169530.167750.20215RANDOM52.491
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]
0.850.420.85-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.914
r_long_range_B_other10.209
r_long_range_B_refined10.206
r_scangle_other8.311
r_dihedral_angle_2_deg7.759
r_dihedral_angle_1_deg6.743
r_mcangle_it6.257
r_mcangle_other6.256
r_scbond_it5.855
r_scbond_other5.854
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.914
r_long_range_B_other10.209
r_long_range_B_refined10.206
r_scangle_other8.311
r_dihedral_angle_2_deg7.759
r_dihedral_angle_1_deg6.743
r_mcangle_it6.257
r_mcangle_other6.256
r_scbond_it5.855
r_scbond_other5.854
r_mcbond_it4.723
r_mcbond_other4.721
r_angle_other_deg1.794
r_angle_refined_deg1.774
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms7516
Nucleic Acid Atoms
Solvent Atoms419
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling