3M67

Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Na-bicine pH 9.0, 2M Na-Malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.972α = 90
b = 41.007β = 104.43
c = 71.681γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBent, vertically focussing mirror2009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8120EMBL/DESY, HAMBURGX13

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
11.840.65699.30.0520.05231.57.5221742201919.3
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)
1.81.9990.2220.22277.63191

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2NNO1.825.1322008220999.320.1810.1760.228RANDOM18.913
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]
-0.040.11-11.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.827
r_dihedral_angle_4_deg17.316
r_dihedral_angle_3_deg14.909
r_dihedral_angle_1_deg6.984
r_scangle_it4.208
r_scbond_it3.017
r_angle_refined_deg2.061
r_mcangle_it2.032
r_mcbond_it1.439
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.827
r_dihedral_angle_4_deg17.316
r_dihedral_angle_3_deg14.909
r_dihedral_angle_1_deg6.984
r_scangle_it4.208
r_scbond_it3.017
r_angle_refined_deg2.061
r_mcangle_it2.032
r_mcbond_it1.439
r_nbtor_refined0.309
r_symmetry_hbond_refined0.244
r_symmetry_vdw_refined0.242
r_nbd_refined0.222
r_xyhbond_nbd_refined0.164
r_chiral_restr0.158
r_metal_ion_refined0.062
r_bond_refined_d0.027
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction