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Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VSM PDB entry 6VSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium malonate, pH 6-7, 6-15% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.675 α = 90 b = 108.675 β = 90 c = 82.948 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 HELIOS MIRRORS 2017-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.9 50 100 0.1087 18.67 17.32 39724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 0.7479 2.58
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 PDB entry 6VSM 1.9 50 39547 1895 99.665 0.17 0.1677 0.1764 0.2219 0.228 24.012
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] -0.113 -0.113 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_4_deg 19.432 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 7.467 r_lrange_it 6.232 r_lrange_other 6.03 r_scangle_it 4.006 r_scangle_other 4.006 r_mcangle_other 2.878 r_mcangle_it 2.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_4_deg 19.432 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 7.467 r_lrange_it 6.232 r_lrange_other 6.03 r_scangle_it 4.006 r_scangle_other 4.006 r_mcangle_other 2.878 r_mcangle_it 2.876 r_scbond_it 2.631 r_scbond_other 2.631 r_mcbond_it 1.968 r_mcbond_other 1.964 r_angle_refined_deg 1.486 r_angle_other_deg 1.404 r_symmetry_xyhbond_nbd_other 0.387 r_nbd_refined 0.228 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_refined 0.186 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.156 r_metal_ion_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.13 r_ncsr_local_group_1 0.118 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3668 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PROTEUM PLUS data reduction PROTEUM PLUS data collection