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De novo retro-aldolase RAbetaB-16.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CZG 6czg,6czj, 6d0t experimental model PDB 6CZJ 6czg,6czj, 6d0t experimental model PDB 6D0T 6czg,6czj, 6d0t
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 2 M ammonium sulfate, 0.1 M Bis-TRIS, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.482 α = 90 b = 77.485 β = 90 c = 60.652 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 2M-F 2021-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.737 45.11 99.96 0.024 0.034 0.024 0.999 17.82 2 13587 24.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 0.565 0.565
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6czg,6czj, 6d0t 1.747 45.11 13587 677 99.904 0.188 0.1865 0.195 0.2257 0.2244 29.35
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] 0.287 0.341 -0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.403 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_2_deg 13.38 r_lrange_it 11.631 r_lrange_other 11.625 r_scangle_it 9.265 r_scangle_other 9.26 r_dihedral_angle_1_deg 5.988 r_scbond_it 5.683 r_scbond_other 5.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.403 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_2_deg 13.38 r_lrange_it 11.631 r_lrange_other 11.625 r_scangle_it 9.265 r_scangle_other 9.26 r_dihedral_angle_1_deg 5.988 r_scbond_it 5.683 r_scbond_other 5.678 r_mcangle_it 3.453 r_mcangle_other 3.453 r_mcbond_it 2.663 r_mcbond_other 2.272 r_angle_refined_deg 1.487 r_angle_other_deg 0.493 r_xyhbond_nbd_refined 0.303 r_nbd_refined 0.204 r_symmetry_nbd_other 0.203 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.184 r_nbd_other 0.159 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 925 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing