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Identification of a New Zinc Binding Chemotype by Fragment Screening
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 the 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 coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.509 α = 90 b = 41.511 β = 104.44 c = 72.172 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2016-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.26 41.5 96.1 0.999 12.5 7.3 63095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 65.1 0.702 2.2 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4cq0 1.27 41.5 59899 3179 97.23 0.12701 0.12585 0.1353 0.14751 0.1568 RANDOM 14.068
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] 0.04 -0.11 0.13 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_sphericity_free 25.138 r_dihedral_angle_4_deg 21.369 r_dihedral_angle_3_deg 11.866 r_sphericity_bonded 9.171 r_dihedral_angle_1_deg 6.465 r_rigid_bond_restr 4.813 r_long_range_B_refined 3.329 r_long_range_B_other 3.329 r_scangle_other 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_sphericity_free 25.138 r_dihedral_angle_4_deg 21.369 r_dihedral_angle_3_deg 11.866 r_sphericity_bonded 9.171 r_dihedral_angle_1_deg 6.465 r_rigid_bond_restr 4.813 r_long_range_B_refined 3.329 r_long_range_B_other 3.329 r_scangle_other 3.05 r_scbond_it 2.718 r_scbond_other 2.718 r_mcangle_other 1.783 r_mcangle_it 1.776 r_angle_refined_deg 1.606 r_mcbond_other 1.383 r_mcbond_it 1.371 r_angle_other_deg 0.978 r_chiral_restr 0.106 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing