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Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VK1 PDB ENTRY 2VK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.35 273.15 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% PEG2000, 11.25% PEG 6000, 1.1MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15K
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.98 α = 90 b = 190.51 β = 113.01 c = 84.14 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 2007-07-08 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 1.42 99 99.7 0.05 22.5 4.4 427276 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 1.42 1.44 99.8 0.63 1.9
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 (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 PDB ENTRY 2VK1 1.42 95.35 425935 1068 99.6 0.181 0.181 0.1796 0.186 0.1841 RANDOM 18.93
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] 0.17 -0.19 -0.06 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 5.39 r_scangle_it 2.592 r_scbond_it 1.67 r_angle_refined_deg 1.25 r_mcangle_it 1.027 r_mcbond_it 0.557 r_chiral_restr 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 5.39 r_scangle_it 2.592 r_scbond_it 1.67 r_angle_refined_deg 1.25 r_mcangle_it 1.027 r_mcbond_it 0.557 r_chiral_restr 0.53 r_nbtor_refined 0.31 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.182 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 17292 Nucleic Acid Atoms Solvent Atoms 1818 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing