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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 8.3 281 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 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.651 α = 90 b = 41.519 β = 104.52 c = 71.931 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 2016-09-27 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 1.53 41.5 99.6 0.997 12.1 7.2 36842
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 1.53 1.56 92.5 0.713 2.3 6.4
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 1.53 69.64 35000 1826 99.48 0.13215 0.12964 0.1291 0.18145 0.1803 RANDOM 14.416
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] -0.19 0.11 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.174 r_dihedral_angle_4_deg 23.142 r_sphericity_free 22.25 r_dihedral_angle_3_deg 14.077 r_sphericity_bonded 8.209 r_dihedral_angle_1_deg 6.248 r_rigid_bond_restr 3.839 r_long_range_B_refined 3.177 r_long_range_B_other 3.177 r_scangle_other 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.174 r_dihedral_angle_4_deg 23.142 r_sphericity_free 22.25 r_dihedral_angle_3_deg 14.077 r_sphericity_bonded 8.209 r_dihedral_angle_1_deg 6.248 r_rigid_bond_restr 3.839 r_long_range_B_refined 3.177 r_long_range_B_other 3.177 r_scangle_other 2.84 r_scbond_it 2.576 r_scbond_other 2.575 r_mcangle_other 1.966 r_mcangle_it 1.937 r_angle_refined_deg 1.914 r_mcbond_it 1.613 r_mcbond_other 1.595 r_angle_other_deg 1.139 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing