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Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZPD PDB ENTRY 1ZPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 VAPOUR DIFFUSION. RESERVIOR CONTAINS FLUORIDE 0.2 M AND PEG3350 20% W/V., PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.78 0.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.901 α = 89.89 b = 111.175 β = 90.87 c = 167.118 γ = 101.27
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 CCD 2007-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 98.1 0.13 11.5 3.7 798597 2.5 26.89
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 2.3 2.35 97.3 0.41 4 3.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1ZPD 2.3 16.97 0.56 423906 21281 95.6 0.172 0.171 0.1679 0.194 0.1891 24.4
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] 1.979 2.6402 -3.4735 3.1308 1.1796 -5.1098
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.156 f_angle_d 0.872 f_chiral_restr 0.061 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34127 Nucleic Acid Atoms Solvent Atoms 4145 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling TRUNCATE data scaling AMoRE phasing