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Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NI5 PDB entry 4NI5
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 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.8 α = 90 b = 108.8 β = 90 c = 83.108 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 2017-12-28 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 1.8 42.025 100 0.0925 21.68 16.99 46796
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 1.8 1.9 0.7928 1.91
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 4NI5 1.8 42.025 46636 2318 99.782 0.163 0.1603 0.1701 0.2095 0.2157 22.962
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] 0.139 0.139 -0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.716 r_dihedral_angle_4_deg 20.824 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 7.613 r_lrange_it 5.776 r_lrange_other 5.54 r_scangle_it 4.047 r_scangle_other 4.046 r_scbond_it 2.683 r_scbond_other 2.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.716 r_dihedral_angle_4_deg 20.824 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 7.613 r_lrange_it 5.776 r_lrange_other 5.54 r_scangle_it 4.047 r_scangle_other 4.046 r_scbond_it 2.683 r_scbond_other 2.682 r_mcangle_it 2.641 r_mcangle_other 2.64 r_mcbond_it 1.928 r_mcbond_other 1.927 r_angle_refined_deg 1.612 r_angle_other_deg 1.485 r_nbd_refined 0.22 r_nbd_other 0.196 r_symmetry_nbd_refined 0.191 r_metal_ion_refined 0.189 r_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.139 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3681 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection PROTEUM PLUS data scaling MOLREP phasing