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Crystal structure of holo-F210W 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 7 277.15 HEPES, Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 1.9 35.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.814 α = 90 b = 70.814 β = 90 c = 221.899 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 2019-05-03 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 1.5 73.97 98.2 0.111 0.148 0.098 0.99 6 3.3 65270
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 1.5 1.53 99.1 0.957 1.278 0.84 0.375 3.3
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 (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 1.5 53.731 65265 3272 98.158 0.186 0.1839 0.1839 0.2254 0.2268 16.909
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] -0.096 -0.048 -0.096 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.407 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.59 r_lrange_it 4.09 r_lrange_other 4.024 r_scangle_it 3.05 r_scangle_other 3.05 r_scbond_it 2.039 r_scbond_other 2.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.407 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.59 r_lrange_it 4.09 r_lrange_other 4.024 r_scangle_it 3.05 r_scangle_other 3.05 r_scbond_it 2.039 r_scbond_other 2.005 r_mcangle_it 1.955 r_mcangle_other 1.955 r_angle_refined_deg 1.582 r_angle_other_deg 1.428 r_mcbond_it 1.337 r_mcbond_other 1.335 r_symmetry_metal_ion_refined 0.587 r_symmetry_nbd_refined 0.448 r_nbd_refined 0.21 r_nbd_other 0.196 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.158 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3753 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing