6YH5

Crystal structure of chimeric carbonic anhydrase XII with 2-Chloro-4-[(pyrimidin-2-ylsulfanyl)acetyl]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
2.0539.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.829α = 90
b = 41.103β = 103.66
c = 71.699γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826605PETRA 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
11.269.67298.80.0490.0570.02215.36.87322973229
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)
11.21.2698.30.2920.2920.3490.1352.76.4

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 REPLACEMENTTHROUGHOUT4Q091.240.6565836736798.670.12660.1230.159RANDOM17.055
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]
-0.48-0.07-0.260.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_sphericity_free25.38
r_dihedral_angle_4_deg16.164
r_dihedral_angle_3_deg12.398
r_sphericity_bonded12.389
r_rigid_bond_restr7.963
r_dihedral_angle_1_deg6.766
r_angle_refined_deg1.997
r_chiral_restr0.141
r_bond_refined_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_sphericity_free25.38
r_dihedral_angle_4_deg16.164
r_dihedral_angle_3_deg12.398
r_sphericity_bonded12.389
r_rigid_bond_restr7.963
r_dihedral_angle_1_deg6.766
r_angle_refined_deg1.997
r_chiral_restr0.141
r_bond_refined_d0.017
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2036
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms35

Software

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