5U0G

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
2.141.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.436α = 90
b = 41.617β = 104.41
c = 72.068γ = 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
11.5441.696.40.99916.47.535191
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)
11.541.5673.30.7692.67.2

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 REPLACEMENTTHROUGHOUT4cq01.5441.633353182296.750.129390.127270.16578RANDOM16.441
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]
0.30.05-0.570.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.972
r_dihedral_angle_4_deg22.522
r_sphericity_free20.569
r_dihedral_angle_3_deg12.027
r_dihedral_angle_1_deg6.42
r_sphericity_bonded5.907
r_long_range_B_other2.414
r_long_range_B_refined2.412
r_rigid_bond_restr1.981
r_scangle_other1.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.972
r_dihedral_angle_4_deg22.522
r_sphericity_free20.569
r_dihedral_angle_3_deg12.027
r_dihedral_angle_1_deg6.42
r_sphericity_bonded5.907
r_long_range_B_other2.414
r_long_range_B_refined2.412
r_rigid_bond_restr1.981
r_scangle_other1.942
r_scbond_it1.747
r_scbond_other1.745
r_mcangle_other1.639
r_mcangle_it1.631
r_angle_refined_deg1.562
r_mcbond_it1.333
r_mcbond_other1.326
r_angle_other_deg0.95
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.008
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 Atoms255
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing