5DOH

Crystal structure of human carbonic anhydrase isozyme II with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291Crystallization buffer: 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.0138.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.162α = 90
b = 41.157β = 104.19
c = 71.854γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826606PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.0569.66189.40.0310.0440.02317.13.81954531954538.491
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.1186.70.2710.2710.380.192.93.727750

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3HLJ1.0569.661954511940489.370.1470.1440.172RANDOM16.924
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]
-0.030.040.01-0.140.020.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_sphericity_free34.178
r_dihedral_angle_4_deg21.717
r_sphericity_bonded16.441
r_dihedral_angle_3_deg12.367
r_rigid_bond_restr9.286
r_dihedral_angle_1_deg6.702
r_angle_refined_deg2.307
r_chiral_restr0.148
r_bond_refined_d0.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_sphericity_free34.178
r_dihedral_angle_4_deg21.717
r_sphericity_bonded16.441
r_dihedral_angle_3_deg12.367
r_rigid_bond_restr9.286
r_dihedral_angle_1_deg6.702
r_angle_refined_deg2.307
r_chiral_restr0.148
r_bond_refined_d0.022
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4118
Nucleic Acid Atoms
Solvent Atoms538
Heterogen Atoms86

Software

Software
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
MOLREPphasing