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Structure of Serratia marcescens 2,3-butanediol dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.31 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.171 α = 90 b = 108.171 β = 90 c = 82.881 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 2017-03-23 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 2 50 100 0.1377 11.23 11.42 33823
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 2 2.1 100 0.6889 1.96 8.77
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 4NI5 2 45.335 33602 1711 99.503 0.165 0.1622 0.1717 0.2141 0.2169 24.025
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] -0.405 -0.405 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 7.462 r_lrange_it 5.646 r_lrange_other 5.478 r_scangle_it 4.011 r_scangle_other 4.011 r_mcangle_it 2.684 r_mcangle_other 2.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_1_deg 7.462 r_lrange_it 5.646 r_lrange_other 5.478 r_scangle_it 4.011 r_scangle_other 4.011 r_mcangle_it 2.684 r_mcangle_other 2.684 r_scbond_it 2.586 r_scbond_other 2.585 r_mcbond_it 1.847 r_mcbond_other 1.846 r_angle_refined_deg 1.497 r_angle_other_deg 1.441 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.212 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_other 0.112 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3661 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection PROTEUM PLUS data scaling MOLREP phasing