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Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-3(P188L).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 1 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl) + 1 uL precipitant (1.2 M sodium citrate, 50 mM TRIS pH 8.0).
Crystal Properties Matthews coefficient Solvent content 3.68 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.37 α = 90 b = 90.37 β = 90 c = 101.81 γ = 90
Symmetry Space Group P 43 21 2
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 2015-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 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 2.1 45.19 99.8 0.073 0.999 19.7 11.8 25229 36.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 98.2 0.76 2 5
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 3KBR 2.1 44.35 23894 1282 99.75 0.17715 0.17556 0.1854 0.20679 0.208 RANDOM 48.698
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_4_deg 20.118 r_dihedral_angle_3_deg 15.517 r_long_range_B_refined 7.753 r_long_range_B_other 7.751 r_dihedral_angle_1_deg 6.6 r_scangle_other 5.9 r_scbond_other 4.026 r_scbond_it 4.023 r_mcangle_other 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_4_deg 20.118 r_dihedral_angle_3_deg 15.517 r_long_range_B_refined 7.753 r_long_range_B_other 7.751 r_dihedral_angle_1_deg 6.6 r_scangle_other 5.9 r_scbond_other 4.026 r_scbond_it 4.023 r_mcangle_other 3.47 r_mcangle_it 3.455 r_mcbond_it 2.629 r_mcbond_other 2.598 r_angle_refined_deg 2.047 r_angle_other_deg 0.918 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1928 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing