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Crystal structure of holo-SwHPA-Mn (hydroxyketoacid aldolase) from Sphingomonas wittichii RW1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo-SwHKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277.15 HEPES, Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.54 α = 90 b = 71.54 β = 90 c = 225.394 γ = 120
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 6M-F 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.65 75.131 99.9 0.15 0.184 0.106 0.99 9.1 5.9 51766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 0.997 1.222 0.69 0.325 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apo-SwHKA 1.65 75.131 51761 2506 99.929 0.161 0.1596 0.1632 0.1931 0.1959 11.952
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] -0.316 -0.316 0.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.423 r_dihedral_angle_3_deg 14.629 r_dihedral_angle_2_deg 9.267 r_dihedral_angle_1_deg 6.135 r_lrange_it 4.763 r_lrange_other 4.511 r_scangle_it 2.789 r_scangle_other 2.788 r_mcangle_other 1.918 r_mcangle_it 1.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.423 r_dihedral_angle_3_deg 14.629 r_dihedral_angle_2_deg 9.267 r_dihedral_angle_1_deg 6.135 r_lrange_it 4.763 r_lrange_other 4.511 r_scangle_it 2.789 r_scangle_other 2.788 r_mcangle_other 1.918 r_mcangle_it 1.916 r_scbond_it 1.906 r_scbond_other 1.876 r_angle_refined_deg 1.869 r_mcbond_it 1.328 r_mcbond_other 1.32 r_angle_other_deg 0.631 r_symmetry_nbd_refined 0.34 r_symmetry_metal_ion_refined 0.254 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.227 r_metal_ion_refined 0.195 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.175 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_other 0.154 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3754 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing