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Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate
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 6.1 281 20MM CITRATE, 10% PEG2000, 10% PEG6000, 5MM TDP, 5MM MAGNESIUM SULFATE, 1MM DTT, 40MM METHYL ACETYLPHOSPHONATE, PH 6.1, 0.95MG KLPDC/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.76 α = 90 b = 135.77 β = 103.88 c = 107.26 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 2006-12-06 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 2.3 99 99.7 0.15 9.6 4.4 100426 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 2.3 2.34 99.9 0.61 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 2G1I 2.3 20.19 99345 1006 99.8 0.154 0.154 0.1534 0.225 0.2252 RANDOM 26.26
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] 0.02 0.69 0.62 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.646 r_dihedral_angle_4_deg 23.335 r_dihedral_angle_3_deg 17.718 r_dihedral_angle_1_deg 7.218 r_scangle_it 4.255 r_scbond_it 2.828 r_mcangle_it 2.033 r_angle_refined_deg 1.952 r_mcbond_it 1.263 r_symmetry_hbond_refined 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.646 r_dihedral_angle_4_deg 23.335 r_dihedral_angle_3_deg 17.718 r_dihedral_angle_1_deg 7.218 r_scangle_it 4.255 r_scbond_it 2.828 r_mcangle_it 2.033 r_angle_refined_deg 1.952 r_mcbond_it 1.263 r_symmetry_hbond_refined 1.027 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.227 r_chiral_restr 0.167 r_xyhbond_nbd_refined 0.155 r_bond_refined_d 0.025 r_gen_planes_refined 0.008 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 17344 Nucleic Acid Atoms Solvent Atoms 1048 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing