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Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VK8 PDB ENTRY 2VK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.35 281 15 MM CITRATE, 1.67 MM MES, 300 MM PYRUVAMIDE, 1.67 MM TDP, 1.67 MM MAGNESIUM SUFATE, 1.67 MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1 MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE, 281 K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.05 α = 89.23 b = 79.22 β = 73.32 c = 109.09 γ = 62.43
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 MARRESEARCH 2007-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 1.6 99 96 0.04 19 1.9 260585 2
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 1.6 1.63 91.6 0.39 2
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 2VK8 1.6 103.7 259466 1070 96 0.181 0.181 0.1807 0.213 0.2127 RANDOM 24.01
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 -0.11 0.64 -0.1 -0.95 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.675 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.766 r_scbond_it 1.832 r_angle_refined_deg 1.345 r_mcangle_it 1.204 r_mcbond_it 0.698 r_chiral_restr 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.675 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.766 r_scbond_it 1.832 r_angle_refined_deg 1.345 r_mcangle_it 1.204 r_mcbond_it 0.698 r_chiral_restr 0.49 r_nbtor_refined 0.311 r_bond_refined_d 0.235 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.201 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.125 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 17113 Nucleic Acid Atoms Solvent Atoms 1413 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing