6T4O

Human Carbonic anhydrase II bound by 3,5-dimethylbenzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Crystallization buffer was 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
2.0840.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.226α = 90
b = 41.325β = 104.31
c = 72.049γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.979700PETRA 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
11.1341.32596.70.0810.0930.03514.76.686341
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)
11.1331.1985.40.1030.1030.1270.056.85.8

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 REPLACEMENTTHROUGHOUT4HT01.13339.8677684864096.470.14170.13890.1661RANDOM15.297
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]
0.37-0.22-0.13-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.742
r_sphericity_free23.343
r_dihedral_angle_4_deg21.56
r_rigid_bond_restr17.228
r_sphericity_bonded15.114
r_dihedral_angle_3_deg10.76
r_dihedral_angle_1_deg6.922
r_angle_refined_deg2.204
r_chiral_restr0.148
r_bond_refined_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.742
r_sphericity_free23.343
r_dihedral_angle_4_deg21.56
r_rigid_bond_restr17.228
r_sphericity_bonded15.114
r_dihedral_angle_3_deg10.76
r_dihedral_angle_1_deg6.922
r_angle_refined_deg2.204
r_chiral_restr0.148
r_bond_refined_d0.017
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2044
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms28

Software

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