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Crystal structure of holo-S116A 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 7.5 292.15 PEG 400, HEPES, Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.03 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.052 α = 90 b = 71.052 β = 90 c = 222.689 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 2.3 74.23 100 0.189 0.215 0.102 0.995 7.5 8.5 18614
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 2.3 2.38 99.9 1.418 1.706 0.934 0.408 6.1
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 2.3 59.31 18594 910 99.882 0.217 0.2149 0.2152 0.2512 0.2513 39.21
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] -0.303 -0.151 -0.303 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.717 r_dihedral_angle_4_deg 14.183 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 6.41 r_lrange_it 4.059 r_lrange_other 4.058 r_scangle_it 2.62 r_scangle_other 2.618 r_mcangle_it 2.383 r_mcangle_other 2.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.717 r_dihedral_angle_4_deg 14.183 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 6.41 r_lrange_it 4.059 r_lrange_other 4.058 r_scangle_it 2.62 r_scangle_other 2.618 r_mcangle_it 2.383 r_mcangle_other 2.382 r_scbond_it 1.558 r_scbond_other 1.542 r_mcbond_it 1.485 r_mcbond_other 1.485 r_angle_refined_deg 1.482 r_angle_other_deg 1.109 r_nbd_refined 0.144 r_symmetry_nbd_other 0.126 r_nbtor_refined 0.125 r_nbd_other 0.121 r_xyhbond_nbd_refined 0.088 r_symmetry_nbd_refined 0.072 r_symmetry_nbtor_other 0.069 r_symmetry_xyhbond_nbd_refined 0.069 r_ncsr_local_group_1 0.069 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3744 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing