6C7W | pdb_00006c7w

Carbonic anhydrase 2 in complex with [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EH5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8281Protein was at 10 mg/mL and was set up in 250 plus 250 nL drops with a reservoir of 50 mM Tris pH 8.0, 2.8 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.238α = 90
b = 41.549β = 104.49
c = 72.237γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102015-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.950100Australian 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
11.2841.699.80.0740.0290.99915.97.262881
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)
11.281.396.30.6810.2850.7592.86.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5eh51.2841.659723313999.780.119060.117410.130.15150.16RANDOM14.74
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]
0.120.08-0.05-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.11
r_sphericity_free31.049
r_dihedral_angle_4_deg22.058
r_dihedral_angle_3_deg12.833
r_sphericity_bonded10.852
r_dihedral_angle_1_deg6.405
r_long_range_B_refined3.497
r_long_range_B_other3.496
r_scangle_other2.633
r_scbond_other2.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.11
r_sphericity_free31.049
r_dihedral_angle_4_deg22.058
r_dihedral_angle_3_deg12.833
r_sphericity_bonded10.852
r_dihedral_angle_1_deg6.405
r_long_range_B_refined3.497
r_long_range_B_other3.496
r_scangle_other2.633
r_scbond_other2.174
r_scbond_it2.173
r_rigid_bond_restr1.933
r_mcangle_other1.887
r_mcangle_it1.862
r_angle_refined_deg1.711
r_mcbond_it1.398
r_mcbond_other1.37
r_angle_other_deg1.007
r_chiral_restr0.111
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2064
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing