4Q81

Crystal structure of 1-hydroxy-4,6-dimethylpyridine-2(1H)-thione bound to human carbonic anhydrase II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KS3PDB entry 3KS3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8291Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0840.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.179α = 90
b = 41.36β = 104.29
c = 72.045γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002013-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5478

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5522.7999.05334493313111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5993.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3KS31.5522.7913344933131175499.050.1760.175430.174090.19984RANDOM12.477
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.296
r_dihedral_angle_4_deg23.571
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.869
r_scangle_it5.311
r_scbond_it3.43
r_mcangle_it2.435
r_angle_refined_deg2.175
r_mcbond_it1.517
r_chiral_restr0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.296
r_dihedral_angle_4_deg23.571
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.869
r_scangle_it5.311
r_scbond_it3.43
r_mcangle_it2.435
r_angle_refined_deg2.175
r_mcbond_it1.517
r_chiral_restr0.159
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms25

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
APEXdata reduction