3S8X

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4-methyl-6-oxo-1,6-dihydro-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION9298Na-Bicine 0.1M pH 9, Na-Malonate 2.2M pH 7, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.208α = 90
b = 41.18β = 104.29
c = 71.918γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMosaic, 225 mmDetector swing-out angle up to 30 degrees2010-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9748EMBL/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
11.341.1895.90.0640.06426.27.65649912.15
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)
11.31.3793.60.380.3827.78022

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 DIFFRACTIONMRTHROUGHOUT3HLJ1.339.845649956478569495.530.1460.1420.179RANDOM16.21
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]
-0.560.540.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_4_deg22.139
r_sphericity_free15.581
r_dihedral_angle_3_deg12.968
r_sphericity_bonded9.391
r_dihedral_angle_1_deg6.606
r_scangle_it6.284
r_scbond_it4.992
r_mcangle_it3.836
r_rigid_bond_restr3.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_4_deg22.139
r_sphericity_free15.581
r_dihedral_angle_3_deg12.968
r_sphericity_bonded9.391
r_dihedral_angle_1_deg6.606
r_scangle_it6.284
r_scbond_it4.992
r_mcangle_it3.836
r_rigid_bond_restr3.305
r_mcbond_it2.928
r_angle_refined_deg2.348
r_nbtor_refined0.322
r_nbd_refined0.226
r_chiral_restr0.191
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.149
r_metal_ion_refined0.083
r_bond_refined_d0.028
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms42

Software

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