5DRS

Crystal structure of human carbonic anhydraseisozyme II with 3-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]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, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Crystal Properties
Matthews coefficientSolvent content
1.9937.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.011α = 90
b = 40.891β = 104.11
c = 71.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826606PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.09940.89195.90.0450.0540.02119.16.291906919069.518
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1679.50.2250.2250.280.1334.611008

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 REPLACEMENTTHROUGHOUT3HLJ1.140.7491885926195.770.1470.1440.173RANDOM17.214
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]
0.13-0.06-0.170.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.148
r_sphericity_free26.282
r_dihedral_angle_4_deg22.551
r_sphericity_bonded14.287
r_dihedral_angle_3_deg12.225
r_rigid_bond_restr9.676
r_dihedral_angle_1_deg7.005
r_angle_refined_deg2.494
r_chiral_restr0.186
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.148
r_sphericity_free26.282
r_dihedral_angle_4_deg22.551
r_sphericity_bonded14.287
r_dihedral_angle_3_deg12.225
r_rigid_bond_restr9.676
r_dihedral_angle_1_deg7.005
r_angle_refined_deg2.494
r_chiral_restr0.186
r_bond_refined_d0.024
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms52

Software

Software
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
MOLREPphasing
Cootmodel building