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Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QPB PDB ENTRY 1QPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.35 273 15MM CITRATE, 1,67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1MG SCPDC/ML PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15C
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.88 α = 90 b = 141.31 β = 107.19 c = 114.41 γ = 90
Symmetry Space Group P 1 21 1
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 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.71 99 99.3 0.07 17.5 3.6 262151 1
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 1.71 1.74 99.2 0.57 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QPB 1.71 109.11 260330 1313 99.1 0.191 0.191 0.22 0.2165 RANDOM 20.91
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] -0.09 -0.32 0.78 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.855 r_dihedral_angle_4_deg 19.513 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 5.714 r_scangle_it 3.295 r_scbond_it 2.193 r_angle_refined_deg 1.45 r_mcangle_it 1.307 r_mcbond_it 0.755 r_chiral_restr 0.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.855 r_dihedral_angle_4_deg 19.513 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 5.714 r_scangle_it 3.295 r_scbond_it 2.193 r_angle_refined_deg 1.45 r_mcangle_it 1.307 r_mcbond_it 0.755 r_chiral_restr 0.514 r_nbtor_refined 0.309 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17280 Nucleic Acid Atoms Solvent Atoms 1558 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing