6YHC

Crystal structure of chimeric carbonic anhydrase XII with 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


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
2.0439.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.89α = 90
b = 40.963β = 103.78
c = 71.406γ = 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)0.976300PETRA 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
11.2840.96398.70.0460.060.0339.23.35996159961
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)
11.281.3598.20.2660.2660.3810.2072.73.3

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 REPLACEMENTTHROUGHOUT4Q091.2840.6853768600298.320.13460.13040.1721RANDOM21.824
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]
-0.660.57-1.211.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.587
r_sphericity_free26.215
r_dihedral_angle_4_deg19.449
r_sphericity_bonded16.288
r_dihedral_angle_3_deg12.884
r_dihedral_angle_1_deg6.985
r_rigid_bond_restr5.444
r_angle_refined_deg2.068
r_chiral_restr0.128
r_gen_planes_refined0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.587
r_sphericity_free26.215
r_dihedral_angle_4_deg19.449
r_sphericity_bonded16.288
r_dihedral_angle_3_deg12.884
r_dihedral_angle_1_deg6.985
r_rigid_bond_restr5.444
r_angle_refined_deg2.068
r_chiral_restr0.128
r_gen_planes_refined0.015
r_bond_refined_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2015
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms59

Software

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