6WKA

human carbonic anhydrase II bound to an inhibitor modified with azidothymidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FLT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2817.5 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C
Crystal Properties
Matthews coefficientSolvent content
2.0941.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.198α = 90
b = 41.521β = 104.358
c = 72.018γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102018-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian 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
11.3441.52950.0780.0310.99914.37.151588
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)
11.341.360.4720.2080.8482.9

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-VALUE5flt1.3439.87551570250994.6590.1290.12670.165811.385
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]
-0.824-0.0920.2710.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.674
r_dihedral_angle_4_deg22.434
r_dihedral_angle_3_deg12.253
r_dihedral_angle_1_deg6.762
r_lrange_it2.873
r_lrange_other2.458
r_scangle_other1.92
r_scangle_it1.919
r_angle_refined_deg1.636
r_mcangle_other1.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.674
r_dihedral_angle_4_deg22.434
r_dihedral_angle_3_deg12.253
r_dihedral_angle_1_deg6.762
r_lrange_it2.873
r_lrange_other2.458
r_scangle_other1.92
r_scangle_it1.919
r_angle_refined_deg1.636
r_mcangle_other1.593
r_mcangle_it1.586
r_scbond_it1.537
r_scbond_other1.537
r_angle_other_deg1.482
r_rigid_bond_restr1.175
r_mcbond_it1.168
r_mcbond_other1.157
r_symmetry_nbd_refined0.317
r_nbd_refined0.238
r_nbd_other0.223
r_symmetry_xyhbond_nbd_refined0.212
r_symmetry_nbd_other0.2
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.174
r_chiral_restr0.091
r_symmetry_nbtor_other0.081
r_metal_ion_refined0.078
r_xyhbond_nbd_other0.016
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing