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Crystal structure of the ancestral amino acid-binding protein AncCDT-1, a precursor of cyclohexadienyl dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 291 A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) was improved by three rounds of serial microseeding; the crystals were crushed and serially diluted in the precipitant, and new hanging drops were prepared by mixing 2 uL protein and 2 uL microseed suspension.
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 90 b = 68.88 β = 90 c = 318.63 γ = 90
Symmetry Space Group P 21 21 21
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 210r 2015-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9501 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.59 33.66 99.4 0.158 0.993 8.2 6.8 33106 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.71 99.3 0.775 0.755 2.4 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZV2 2.59 33.19 31387 1686 98.87 0.25518 0.25348 0.28733 0.2692 RANDOM 43.419
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] 2.35 0.55 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.911 r_dihedral_angle_3_deg 18.623 r_dihedral_angle_4_deg 13.699 r_dihedral_angle_1_deg 6.038 r_long_range_B_refined 3.106 r_long_range_B_other 3.103 r_mcangle_it 1.86 r_mcangle_other 1.859 r_scangle_other 1.5 r_angle_refined_deg 1.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.911 r_dihedral_angle_3_deg 18.623 r_dihedral_angle_4_deg 13.699 r_dihedral_angle_1_deg 6.038 r_long_range_B_refined 3.106 r_long_range_B_other 3.103 r_mcangle_it 1.86 r_mcangle_other 1.859 r_scangle_other 1.5 r_angle_refined_deg 1.372 r_angle_other_deg 1.195 r_mcbond_other 1.046 r_mcbond_it 1.045 r_scbond_it 0.836 r_scbond_other 0.836 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6937 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing