5VGY

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 DROP8.3281concentrated CA II at 10 mg/mL was set up with microseeding over 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3 at 8 C in 250 nL plus 225 nL plus 25 nL (seeds) ratio.
Crystal Properties
Matthews coefficientSolvent content
2.1141.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.454α = 90
b = 41.654β = 104.29
c = 72.045γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953700Australian 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
11.3941.697.50.0710.0280.99918.17.447924
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)
11.391.4293.70.7570.30.7762.67.1

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 REPLACEMENTTHROUGHOUT4cq01.3941.645561235297.50.115010.11290.15646RANDOM15.279
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]
0.050.070.08-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.112
r_sphericity_free31.644
r_dihedral_angle_4_deg21.619
r_dihedral_angle_3_deg12.358
r_sphericity_bonded9.975
r_dihedral_angle_1_deg6.477
r_long_range_B_refined3.429
r_long_range_B_other3.429
r_scangle_other2.886
r_mcangle_other2.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.112
r_sphericity_free31.644
r_dihedral_angle_4_deg21.619
r_dihedral_angle_3_deg12.358
r_sphericity_bonded9.975
r_dihedral_angle_1_deg6.477
r_long_range_B_refined3.429
r_long_range_B_other3.429
r_scangle_other2.886
r_mcangle_other2.779
r_mcangle_it2.767
r_rigid_bond_restr2.67
r_scbond_it2.495
r_scbond_other2.494
r_mcbond_it2.193
r_mcbond_other2.184
r_angle_refined_deg1.906
r_angle_other_deg1.043
r_chiral_restr0.295
r_bond_refined_d0.018
r_gen_planes_refined0.011
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 Atoms2054
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing