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Pyruvate decarboxylase from Kluyveromyces lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VK4 PDB entry 2VK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 281.15 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 30 seconds in 2 uL mother liquor + 2 uL 15% w/v glycerol, 200 mM acetaldehyde prior to flash freezing.
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.36 α = 80.1 b = 78.48 β = 67.72 c = 100.57 γ = 77.4
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 MARMOSAIC 225 mm CCD 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.00001 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.04 38.25 93.2 0.086 0.109 0.065 0.996 8.6 2.7 126964 24.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.08 66.8 0.659 0.837 0.508 0.689 1.7 2.3
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 2VK4 2.04 38.25 125994 970 93.15 0.22123 0.22069 0.2261 0.2903 0.2912 RANDOM 37.997
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] -1.7 -1.22 -0.76 -1.37 0.62 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.903 r_dihedral_angle_4_deg 18.943 r_dihedral_angle_3_deg 17.669 r_dihedral_angle_1_deg 7.726 r_long_range_B_refined 7.014 r_long_range_B_other 7.014 r_scangle_other 4.719 r_mcangle_it 4.402 r_mcangle_other 4.401 r_scbond_it 3.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.903 r_dihedral_angle_4_deg 18.943 r_dihedral_angle_3_deg 17.669 r_dihedral_angle_1_deg 7.726 r_long_range_B_refined 7.014 r_long_range_B_other 7.014 r_scangle_other 4.719 r_mcangle_it 4.402 r_mcangle_other 4.401 r_scbond_it 3.095 r_scbond_other 3.095 r_mcbond_it 2.98 r_mcbond_other 2.98 r_angle_refined_deg 1.422 r_angle_other_deg 0.919 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 16531 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling MOLREP phasing