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Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate
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 7.5 292.15 PEG400, HEPES, Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.327 α = 90 b = 71.327 β = 90 c = 223.185 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 2020-11-17 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 1.8 74.39 98.5 0.101 0.132 0.085 0.997 8.5 3.4 38705
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 1.8 1.84 99 1.196 1.589 1.037 0.365 3.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6R62 1.8 59.533 38701 1936 98.533 0.185 0.1831 0.2247 0.2053 22.099
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] -0.165 -0.083 -0.165 0.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.644 r_dihedral_angle_4_deg 14.454 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_1_deg 6.954 r_lrange_it 4.351 r_lrange_other 4.185 r_scangle_it 3.139 r_scangle_other 3.138 r_mcangle_it 2.113 r_mcangle_other 2.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.644 r_dihedral_angle_4_deg 14.454 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_1_deg 6.954 r_lrange_it 4.351 r_lrange_other 4.185 r_scangle_it 3.139 r_scangle_other 3.138 r_mcangle_it 2.113 r_mcangle_other 2.112 r_scbond_it 2.083 r_scbond_other 2.074 r_angle_refined_deg 1.666 r_mcbond_it 1.529 r_mcbond_other 1.525 r_angle_other_deg 1.343 r_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_other 0.146 r_nbtor_refined 0.142 r_xyhbond_nbd_refined 0.14 r_nbd_other 0.122 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.073 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.003 r_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3731 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing