7M23

Human carbonic anhydrase II in complex with troglitazone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ODZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3293Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3.
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.333α = 90
b = 41.292β = 104.356
c = 71.688γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953656Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.341.2999.10.0710.0450.99812.26.658740
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.320.6270.4160.825

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6odz1.339.94358729290099.1120.1220.12040.15114.036
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]
-0.295-0.669-1.031.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.238
r_dihedral_angle_4_deg20.433
r_dihedral_angle_3_deg11.887
r_dihedral_angle_1_deg7.132
r_lrange_it2.961
r_lrange_other2.689
r_scangle_it2.515
r_scangle_other2.514
r_rigid_bond_restr2.063
r_scbond_it2.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.238
r_dihedral_angle_4_deg20.433
r_dihedral_angle_3_deg11.887
r_dihedral_angle_1_deg7.132
r_lrange_it2.961
r_lrange_other2.689
r_scangle_it2.515
r_scangle_other2.514
r_rigid_bond_restr2.063
r_scbond_it2.017
r_scbond_other2.013
r_mcangle_other1.86
r_mcangle_it1.856
r_angle_refined_deg1.608
r_angle_other_deg1.452
r_mcbond_it1.446
r_mcbond_other1.446
r_nbd_refined0.245
r_symmetry_nbd_refined0.245
r_symmetry_xyhbond_nbd_refined0.219
r_nbd_other0.21
r_symmetry_nbd_other0.201
r_xyhbond_nbd_refined0.199
r_nbtor_refined0.175
r_xyhbond_nbd_other0.125
r_chiral_restr0.092
r_symmetry_nbtor_other0.083
r_metal_ion_refined0.048
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing