7M24

Human carbonic anhydrase II in complex with (R)-rosiglitazone


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
2.0941.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.574α = 90
b = 41.282β = 104.416
c = 71.932γ = 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
11.341.2899.70.0640.040.99914.66.659530
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)
11.31.320.4430.2940.865

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-VALUE6ODZ1.340.16559512293599.6270.1170.11580.145712.774
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]
-0.2530.173-0.4390.533
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.99
r_dihedral_angle_4_deg21.366
r_dihedral_angle_3_deg11.457
r_dihedral_angle_1_deg7.161
r_lrange_it2.777
r_lrange_other2.288
r_scangle_it2.027
r_scangle_other2.027
r_angle_refined_deg1.623
r_scbond_it1.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.99
r_dihedral_angle_4_deg21.366
r_dihedral_angle_3_deg11.457
r_dihedral_angle_1_deg7.161
r_lrange_it2.777
r_lrange_other2.288
r_scangle_it2.027
r_scangle_other2.027
r_angle_refined_deg1.623
r_scbond_it1.556
r_scbond_other1.556
r_mcangle_other1.527
r_mcangle_it1.525
r_angle_other_deg1.468
r_rigid_bond_restr1.156
r_mcbond_other1.136
r_mcbond_it1.135
r_symmetry_nbd_refined0.255
r_nbd_refined0.233
r_xyhbond_nbd_refined0.208
r_symmetry_nbd_other0.197
r_nbd_other0.197
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.161
r_symmetry_xyhbond_nbd_other0.125
r_chiral_restr0.09
r_symmetry_nbtor_other0.081
r_metal_ion_refined0.064
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms313
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing