3M96

Crystal structure of human carbonic anhydrase isozyme II with 5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate and 2M sodium malonate, pH 7.0 made from 1M sodium BICINE and 3.4M sodium malonate, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0439.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.05α = 90
b = 40.921β = 104.14
c = 71.468γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9443EMBL/DESY, HAMBURGX12

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
11.428.88499.20.0950.09522.99.3466704629714.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4898.10.2530.2534.47.46614

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3HLJ1.428.474667046284464799.230.180.1760.213RANDOM15.552
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]
0.120.11-0.510.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_4_deg22.122
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg6.952
r_scangle_it4.879
r_scbond_it3.309
r_angle_refined_deg2.587
r_mcangle_it2.474
r_mcbond_it1.84
r_nbtor_refined0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_4_deg22.122
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg6.952
r_scangle_it4.879
r_scbond_it3.309
r_angle_refined_deg2.587
r_mcangle_it2.474
r_mcbond_it1.84
r_nbtor_refined0.325
r_nbd_refined0.226
r_symmetry_hbond_refined0.212
r_symmetry_vdw_refined0.187
r_chiral_restr0.186
r_xyhbond_nbd_refined0.15
r_metal_ion_refined0.078
r_bond_refined_d0.032
r_gen_planes_refined0.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection