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Crystal structure of holo-H44A mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R62
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 2.03 39.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.881 α = 90 b = 70.881 β = 90 c = 223.18 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 2019-04-26 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 1.85 59.19 94 0.153 0.18 0.094 0.996 4.6 3.8 33572
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 1.85 1.89 1.537 1.801 0.916 0.602 3.7
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 6R62 1.85 59.19 33393 1714 93.417 0.16 0.158 0.1553 0.1959 0.1912 27.832
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] 0.054 0.027 0.054 -0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_4_deg 17.75 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 6.614 r_lrange_it 5.31 r_lrange_other 5.253 r_scangle_it 3.876 r_scangle_other 3.875 r_mcangle_it 2.687 r_mcangle_other 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_4_deg 17.75 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 6.614 r_lrange_it 5.31 r_lrange_other 5.253 r_scangle_it 3.876 r_scangle_other 3.875 r_mcangle_it 2.687 r_mcangle_other 2.686 r_scbond_it 2.56 r_scbond_other 2.56 r_mcbond_it 1.885 r_mcbond_other 1.884 r_angle_refined_deg 1.443 r_angle_other_deg 1.342 r_symmetry_metal_ion_refined 0.405 r_symmetry_nbd_refined 0.322 r_metal_ion_refined 0.23 r_nbd_refined 0.214 r_nbd_other 0.196 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3736 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing