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Alpha-ketoisovalerate decarboxylase (KivD) from Lactococcus lactis, thermostable mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20mM MES pH6.8, 2.5mM MgSO4, 0.1mM TPP(ThDP), 1mM DTT, 20% PEG3000, 0.2M NaCl, 0.1M HEPES/NaOH pH7.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.195 α = 90 b = 128.268 β = 90 c = 147.737 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M-F 2017-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97930 APS 24-ID-C
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 1.8 100 99.4 0.151 0.16 0.051 6.4 8.8 223094
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 1.8 1.86 97.2 1.055 1.124 0.379 0.698 7.9
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 2VBF 1.8 96.856 222993 11416 99.235 0.184 0.1828 0.1901 0.2104 0.2143 35.974
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] -0.482 1.524 -1.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 6.958 r_lrange_it 5.637 r_lrange_other 5.576 r_scangle_it 4.599 r_scangle_other 4.599 r_scbond_other 3.341 r_scbond_it 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 6.958 r_lrange_it 5.637 r_lrange_other 5.576 r_scangle_it 4.599 r_scangle_other 4.599 r_scbond_other 3.341 r_scbond_it 3.34 r_mcangle_it 3.327 r_mcangle_other 3.327 r_mcbond_it 2.605 r_mcbond_other 2.603 r_angle_refined_deg 1.423 r_angle_other_deg 1.394 r_nbd_other 0.216 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.076 r_ncsr_local_group_1 0.057 r_ncsr_local_group_6 0.057 r_ncsr_local_group_3 0.056 r_ncsr_local_group_2 0.052 r_ncsr_local_group_4 0.051 r_ncsr_local_group_5 0.049 r_metal_ion_refined 0.021 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16647 Nucleic Acid Atoms Solvent Atoms 1181 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction