5LL4

Crystal structure of human carbonic anhydrase isozyme II with 4-(1H-benzimidazol-1-ylacetyl)benzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Crystal Properties
Matthews coefficientSolvent content
2.0238.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.11α = 90
b = 41.174β = 104.21
c = 72.084γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.826606PETRA III, EMBL c/o DESYP14 (MX2)

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
11.1241.17480.70.03516.33.8144738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1849.30.1574.33.6

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 REPLACEMENTTHROUGHOUT3HLJ1.1241.17137528720480.790.13320.13120.1713RANDOM17.837
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]
0.01-0.060.020.140.05-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.266
r_sphericity_free29.905
r_dihedral_angle_4_deg22.98
r_sphericity_bonded16.441
r_dihedral_angle_3_deg12.789
r_rigid_bond_restr8.904
r_dihedral_angle_1_deg6.955
r_angle_refined_deg2.247
r_chiral_restr0.17
r_bond_refined_d0.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.266
r_sphericity_free29.905
r_dihedral_angle_4_deg22.98
r_sphericity_bonded16.441
r_dihedral_angle_3_deg12.789
r_rigid_bond_restr8.904
r_dihedral_angle_1_deg6.955
r_angle_refined_deg2.247
r_chiral_restr0.17
r_bond_refined_d0.023
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4124
Nucleic Acid Atoms
Solvent Atoms652
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing