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Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G1I PDB ENTRY 2G1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.45 281 50MM MES, 1MM DTT, 5MM TDP, 5MM MAGNESIUM SULFATE, 10% PEG 2000, 10% PEG 8000, 2MG KLPDC/ML, PH 6.45, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.709 α = 90 b = 203.175 β = 91.81 c = 79.815 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 MARRESEARCH 2005-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.95 48.45 86.3 0.1 11.5 4.3 155315 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 1.95 2.06 80.6 0.51 2.5
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 2G1I 1.95 48.45 147446 7784 100 0.18 0.178 0.1771 0.23 0.2291 RANDOM 22.08
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] -0.06 -0.06 0.26 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.346 r_dihedral_angle_4_deg 21.703 r_dihedral_angle_3_deg 16.696 r_dihedral_angle_1_deg 6.596 r_scangle_it 3.772 r_scbond_it 2.512 r_angle_refined_deg 1.85 r_mcangle_it 1.588 r_mcbond_it 0.929 r_chiral_restr 0.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.346 r_dihedral_angle_4_deg 21.703 r_dihedral_angle_3_deg 16.696 r_dihedral_angle_1_deg 6.596 r_scangle_it 3.772 r_scbond_it 2.512 r_angle_refined_deg 1.85 r_mcangle_it 1.588 r_mcbond_it 0.929 r_chiral_restr 0.441 r_nbtor_refined 0.308 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.144 r_bond_refined_d 0.019 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 17227 Nucleic Acid Atoms Solvent Atoms 1319 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing