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Zymomonas mobilis pyruvate decarboxylase mutant PDC-2.3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M MES monohydrate pH 6.0, 2.4 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.44 α = 90 b = 124.44 β = 90 c = 173.825 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 2016-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54188
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 1.67 101.18 99.8 0.0721 16.57 10.41 157603
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 98.6 0.7867 16.57 4.98
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 (Observed) 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 2wvg 1.67 101.18 149303 7707 99.47 0.17201 0.17038 0.1809 0.20269 0.209 RANDOM 24.692
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_4_deg 19.069 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 6.37 r_long_range_B_refined 6.055 r_long_range_B_other 5.932 r_scangle_other 4.729 r_scbond_it 3.214 r_scbond_other 3.214 r_mcangle_it 2.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_4_deg 19.069 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 6.37 r_long_range_B_refined 6.055 r_long_range_B_other 5.932 r_scangle_other 4.729 r_scbond_it 3.214 r_scbond_other 3.214 r_mcangle_it 2.968 r_mcangle_other 2.968 r_mcbond_it 2.233 r_mcbond_other 2.232 r_angle_refined_deg 1.942 r_angle_other_deg 1.086 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8567 Nucleic Acid Atoms Solvent Atoms 1004 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Coot model building PROTEUM PLUS data scaling