4WL4

Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P58 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82961.6 M sodium citrate, Tris 50 mM
Crystal Properties
Matthews coefficientSolvent content
2.0941.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.264α = 90
b = 41.367β = 104.21
c = 72.276γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.000ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.129.180.70.0480.05712.93.4578925-315.075
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1727.20.4210.5541.73

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 REPLACEMENTTHROUGHOUT3P581.129.175094381480.740.110.1090.1299RANDOM15.743
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]
0.24-0.08-0.15-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.448
r_dihedral_angle_2_deg34.193
r_dihedral_angle_4_deg24.683
r_sphericity_bonded11.081
r_dihedral_angle_3_deg10.739
r_dihedral_angle_1_deg6.406
r_mcangle_it1.678
r_angle_refined_deg1.311
r_mcbond_it1.196
r_mcbond_other1.195
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.448
r_dihedral_angle_2_deg34.193
r_dihedral_angle_4_deg24.683
r_sphericity_bonded11.081
r_dihedral_angle_3_deg10.739
r_dihedral_angle_1_deg6.406
r_mcangle_it1.678
r_angle_refined_deg1.311
r_mcbond_it1.196
r_mcbond_other1.195
r_rigid_bond_restr1.079
r_angle_other_deg0.787
r_chiral_restr0.086
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2027
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing
XSCALEdata reduction