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Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 Protein was concentrated to 4.2 mg/mL; reservoir was 20% PEG 3350 and 0.2 M magnesium acetate at 8 C; drops were 150 nL protein plus 150 nL reservoir.
Crystal Properties Matthews coefficient Solvent content 2.1 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.762 α = 90 b = 105.799 β = 90 c = 299.127 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 315r 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.56 46.7 99.5 12.5 7.5 95206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.6 98.9 1.8 7.6
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 5HY0 2.56 46.7 90462 4666 99.38 0.2311 0.22943 0.2316 0.26343 0.2629 RANDOM 53.899
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] -0.58 -1.37 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.808 r_dihedral_angle_4_deg 19.431 r_dihedral_angle_3_deg 14.658 r_long_range_B_other 11.375 r_long_range_B_refined 11.373 r_dihedral_angle_1_deg 7.244 r_mcangle_it 6.846 r_mcangle_other 6.846 r_scangle_other 6.243 r_mcbond_it 4.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.808 r_dihedral_angle_4_deg 19.431 r_dihedral_angle_3_deg 14.658 r_long_range_B_other 11.375 r_long_range_B_refined 11.373 r_dihedral_angle_1_deg 7.244 r_mcangle_it 6.846 r_mcangle_other 6.846 r_scangle_other 6.243 r_mcbond_it 4.378 r_mcbond_other 4.377 r_scbond_it 3.923 r_scbond_other 3.923 r_angle_other_deg 2.097 r_angle_refined_deg 1.522 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_bond_other_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.009 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 19446 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing