3SBI | pdb_00003sbi

Crystal structure of human carbonic anhydrase isozyme II with 4-[(2-pyrimidinylsulfanyl)acetyl]benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION92930.1M Na-bicine pH 9, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.141.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.348α = 90
b = 41.314β = 104.25
c = 72.24γ = 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 mirrors2010-11-12MSINGLE 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 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
11.420.6897.10.0430.04325.264646712.4
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)
11.41.4895.70.3440.344266675

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTPDB entry 3HLJ1.420.664645146451470596.880.1380.1380.1330.12880.1830.1796RANDOM14.597
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]
0.21-0.05-0.19-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.908
r_dihedral_angle_4_deg22.742
r_sphericity_free13.699
r_dihedral_angle_3_deg12.767
r_sphericity_bonded7.853
r_dihedral_angle_1_deg6.795
r_scangle_it5.924
r_scbond_it4.662
r_mcangle_it3.637
r_rigid_bond_restr3.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.908
r_dihedral_angle_4_deg22.742
r_sphericity_free13.699
r_dihedral_angle_3_deg12.767
r_sphericity_bonded7.853
r_dihedral_angle_1_deg6.795
r_scangle_it5.924
r_scbond_it4.662
r_mcangle_it3.637
r_rigid_bond_restr3.065
r_mcbond_it2.721
r_angle_refined_deg2.234
r_nbtor_refined0.313
r_nbd_refined0.234
r_symmetry_vdw_refined0.202
r_symmetry_hbond_refined0.197
r_chiral_restr0.182
r_xyhbond_nbd_refined0.166
r_metal_ion_refined0.034
r_bond_refined_d0.029
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms40

Software

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