☰ Navigation Tabs
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 5HXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Protein was at 15 mg/mL; reservoir was 2.5 M ammonium sulfate, 0.1 M bis-tris at pH 6.5; vapor diffusion sitting drops of 150 nL plus 150 nL; done at 20 C.
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.63 α = 90 b = 83.732 β = 90 c = 215.102 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 2014-03-30 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 2.36 45.3 99.9 8 7.4 61689
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 2.36 2.42 98.6 2.6 7.3
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 5hxu 2.36 45.3 58648 2963 99.87 0.22578 0.22428 0.2233 0.25516 0.2541 RANDOM 31.438
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] 0.57 0.83 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.62 r_dihedral_angle_4_deg 16.102 r_dihedral_angle_3_deg 14.78 r_long_range_B_refined 6.61 r_long_range_B_other 6.61 r_scangle_other 6.066 r_dihedral_angle_1_deg 5.389 r_scbond_it 4.934 r_scbond_other 4.932 r_mcangle_it 4.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.62 r_dihedral_angle_4_deg 16.102 r_dihedral_angle_3_deg 14.78 r_long_range_B_refined 6.61 r_long_range_B_other 6.61 r_scangle_other 6.066 r_dihedral_angle_1_deg 5.389 r_scbond_it 4.934 r_scbond_other 4.932 r_mcangle_it 4.658 r_mcangle_other 4.658 r_mcbond_it 3.729 r_mcbond_other 3.728 r_angle_other_deg 3.649 r_angle_refined_deg 1.136 r_chiral_restr 0.038 r_bond_refined_d 0.006 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_other_d 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 10839 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing