3SAX

Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-{[(5-ethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92980.1M Na-bicine pH 9, 2.6M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0840.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.221α = 90
b = 41.172β = 104.2
c = 72.197γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirror Bent, vertically focussing2010-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.141.17293.40.06815.57.2927097.8
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)
11.11.1579.20.2750.2752.65.511403

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 DIFFRACTIONMRTHROUGHOUTPDB entry 3HLJ1.135.499266892668925594.630.1290.1290.1260.158RANDOM12.365
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]
-0.430.060.30.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.029
r_dihedral_angle_4_deg20.752
r_sphericity_free15.369
r_dihedral_angle_3_deg11.375
r_dihedral_angle_1_deg7.366
r_sphericity_bonded5.806
r_scangle_it5.679
r_scbond_it4.371
r_angle_other_deg4.325
r_mcbond_other3.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.029
r_dihedral_angle_4_deg20.752
r_sphericity_free15.369
r_dihedral_angle_3_deg11.375
r_dihedral_angle_1_deg7.366
r_sphericity_bonded5.806
r_scangle_it5.679
r_scbond_it4.371
r_angle_other_deg4.325
r_mcbond_other3.968
r_mcangle_it3.382
r_rigid_bond_restr3.279
r_angle_refined_deg2.524
r_mcbond_it2.522
r_symmetry_vdw_refined0.286
r_symmetry_vdw_other0.277
r_nbd_refined0.276
r_nbd_other0.258
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.202
r_nbtor_refined0.187
r_chiral_restr0.153
r_nbtor_other0.112
r_metal_ion_refined0.081
r_bond_refined_d0.029
r_gen_planes_other0.018
r_gen_planes_refined0.014
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms43

Software

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