5U0D

Identification of a New Zinc Binding Chemotype by Fragment Screening


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CQ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP281the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Crystal Properties
Matthews coefficientSolvent content
2.141.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.567α = 90
b = 41.341β = 104.47
c = 72.094γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102016-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953700Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.5941.399.60.99921.67.232975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.6193.60.863.56.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4cq01.5941.331243171999.60.120450.118480.15449RANDOM15.669
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]
0.18-0.01-0.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg23.204
r_sphericity_free20.746
r_dihedral_angle_3_deg11.981
r_sphericity_bonded7.292
r_dihedral_angle_1_deg6.417
r_long_range_B_refined2.811
r_long_range_B_other2.81
r_scangle_other2.457
r_scbond_it2.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg23.204
r_sphericity_free20.746
r_dihedral_angle_3_deg11.981
r_sphericity_bonded7.292
r_dihedral_angle_1_deg6.417
r_long_range_B_refined2.811
r_long_range_B_other2.81
r_scangle_other2.457
r_scbond_it2.107
r_scbond_other2.107
r_rigid_bond_restr1.816
r_mcangle_other1.747
r_mcangle_it1.729
r_angle_refined_deg1.516
r_mcbond_it1.396
r_mcbond_other1.36
r_angle_other_deg0.917
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2059
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing