6YH8

Crystal structure of chimeric carbonic anhydrase XII with 2-[(1S)-1,2,3,4-Tetrahydronapthalen-1-ylamino)-3,5,6-trifluorobenzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q09 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Crystallization buffer was 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
2.0539.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.035α = 90
b = 41.044β = 103.93
c = 71.429γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97630PETRA 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
11.240.79896.50.0380.0490.02119.95.17122871228
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)
11.21.2693.10.1560.1560.1950.0864.85

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 REPLACEMENTTHROUGHOUT4Q091.239.5763953725796.140.13930.13560.1721RANDOM17.256
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]
0.4-0.12-0.590.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.858
r_sphericity_free25.588
r_dihedral_angle_4_deg17.41
r_sphericity_bonded16.291
r_dihedral_angle_3_deg13.602
r_dihedral_angle_1_deg7.308
r_rigid_bond_restr7.018
r_angle_refined_deg2.283
r_chiral_restr0.154
r_gen_planes_refined0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.858
r_sphericity_free25.588
r_dihedral_angle_4_deg17.41
r_sphericity_bonded16.291
r_dihedral_angle_3_deg13.602
r_dihedral_angle_1_deg7.308
r_rigid_bond_restr7.018
r_angle_refined_deg2.283
r_chiral_restr0.154
r_gen_planes_refined0.016
r_bond_refined_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2025
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms40

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Cootmodel building