4KNM

Crystal structure of human carbonic anhydrase isozyme XIII with 2-Chloro-4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NNO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52910.1M sodium citrate (pH 5.5), 0.1M sodium acetate (pH 4.5), 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
239.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.591α = 90
b = 58.165β = 92.16
c = 71.075γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2011-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.8520.54299.70.0830.08316.14.23711425.023
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)
11.92990.4670.4670.620.31.345374

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2NNO1.920.463709937099365399.740.1840.1840.1780.235RANDOM21.671
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]
-0.310.8-0.360.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.93
r_dihedral_angle_3_deg15.282
r_dihedral_angle_4_deg13.4
r_dihedral_angle_1_deg7.318
r_scangle_it4.251
r_scbond_it2.927
r_angle_refined_deg1.988
r_mcangle_it1.912
r_mcbond_it1.192
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.93
r_dihedral_angle_3_deg15.282
r_dihedral_angle_4_deg13.4
r_dihedral_angle_1_deg7.318
r_scangle_it4.251
r_scbond_it2.927
r_angle_refined_deg1.988
r_mcangle_it1.912
r_mcbond_it1.192
r_nbtor_refined0.307
r_symmetry_vdw_refined0.244
r_nbd_refined0.21
r_symmetry_hbond_refined0.179
r_metal_ion_refined0.161
r_xyhbond_nbd_refined0.159
r_chiral_restr0.146
r_bond_refined_d0.023
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4116
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
DNAdata collection
MOLREPphasing