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Structure of a Bacillus coagulans polyol dehydrogenase double mutant with an acquired D-lactate dehydrogenase activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 0.2M Ammonium citrate dibasic, 10% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.672 α = 90 b = 211.772 β = 90 c = 149.43 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315r Sagittal focusing 2nd crystal horizontal focusing 2014-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.39 149.71 96.07 0.136 0.148 0.057 5.1 6.3 126258
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 2.4 2.44 97.2 0.494 0.539 0.21 0.904 2.3 6.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KQ3 2.395 149.71 126258 6235 96.071 0.239 0.2374 0.2425 0.2687 0.2731 RANDOM 27.388
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] -1.451 -2.035 3.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.285 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 13.604 r_lrange_other 6.97 r_lrange_it 6.968 r_scangle_it 5.921 r_scangle_other 5.921 r_dihedral_angle_1_deg 5.539 r_scbond_it 3.958 r_scbond_other 3.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.285 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 13.604 r_lrange_other 6.97 r_lrange_it 6.968 r_scangle_it 5.921 r_scangle_other 5.921 r_dihedral_angle_1_deg 5.539 r_scbond_it 3.958 r_scbond_other 3.958 r_mcangle_it 3.94 r_mcangle_other 3.94 r_mcbond_it 2.702 r_mcbond_other 2.701 r_angle_refined_deg 1.274 r_angle_other_deg 0.918 r_symmetry_xyhbond_nbd_refined 0.277 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.189 r_nbd_other 0.179 r_nbtor_refined 0.16 r_symmetry_nbd_other 0.135 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_other 0.063 r_ncsr_local_group_13 0.049 r_ncsr_local_group_24 0.048 r_ncsr_local_group_6 0.047 r_ncsr_local_group_9 0.047 r_ncsr_local_group_12 0.047 r_ncsr_local_group_3 0.046 r_ncsr_local_group_5 0.046 r_ncsr_local_group_7 0.046 r_ncsr_local_group_17 0.046 r_ncsr_local_group_23 0.046 r_ncsr_local_group_19 0.045 r_ncsr_local_group_25 0.045 r_ncsr_local_group_11 0.044 r_ncsr_local_group_14 0.044 r_ncsr_local_group_18 0.043 r_ncsr_local_group_16 0.042 r_ncsr_local_group_10 0.036 r_ncsr_local_group_21 0.036 r_ncsr_local_group_28 0.036 r_ncsr_local_group_2 0.033 r_ncsr_local_group_26 0.033 r_ncsr_local_group_15 0.032 r_ncsr_local_group_8 0.031 r_ncsr_local_group_20 0.031 r_ncsr_local_group_4 0.03 r_ncsr_local_group_1 0.029 r_ncsr_local_group_22 0.027 r_ncsr_local_group_27 0.027 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22070 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing