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Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide
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 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing
Crystal Properties Matthews coefficient Solvent content 3.22 61.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.765 α = 90 b = 172.765 β = 90 c = 210.083 γ = 90
Symmetry Space Group I 4 2 2
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 QUANTUM 4 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 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 2.99 55.6 100 0.333 9 14.4 32279 25.68
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 2.99 3.05 100 1.797 1.6 14.7
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 2.99 55.6 31223 1055 100 0.181 0.178 0.1846 0.265 0.2627 RANDOM 42.52
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] 1.94 1.94 -3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.609 r_dihedral_angle_4_deg 20.327 r_dihedral_angle_3_deg 19.268 r_dihedral_angle_1_deg 8.406 r_long_range_B_refined 7.526 r_long_range_B_other 7.526 r_mcangle_it 5.17 r_mcangle_other 5.169 r_scangle_other 4.882 r_mcbond_it 3.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.609 r_dihedral_angle_4_deg 20.327 r_dihedral_angle_3_deg 19.268 r_dihedral_angle_1_deg 8.406 r_long_range_B_refined 7.526 r_long_range_B_other 7.526 r_mcangle_it 5.17 r_mcangle_other 5.169 r_scangle_other 4.882 r_mcbond_it 3.213 r_mcbond_other 3.2 r_scbond_it 2.985 r_scbond_other 2.985 r_angle_refined_deg 1.465 r_angle_other_deg 0.859 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 8587 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement xia2 data reduction MOSFLM data reduction Aimless data scaling MOLREP phasing