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The complex structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis with 2R-1-hydroxyethyl-deazaThDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBF PDB ENTRY 2VBF
Crystallization Crystal Properties Matthews coefficient Solvent content 1.95 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.977 α = 90 b = 108.578 β = 90 c = 146.529 γ = 90
Symmetry Space Group P 21 21 21
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 CCD TOROIDAL MIRROR 2007-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.8 56.34 97.4 0.09 13.1 3.6 95616 6
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 1.8 1.9 85.2 0.38 2.1 2.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VBF 1.8 30 90719 4792 97.3 0.165 0.163 0.205 RANDOM 12.25
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] -0.37 -0.99 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.382 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_3_deg 12.391 r_dihedral_angle_1_deg 5.515 r_scangle_it 2.103 r_scbond_it 1.301 r_angle_refined_deg 1.131 r_angle_other_deg 0.897 r_mcangle_it 0.821 r_mcbond_it 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.382 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_3_deg 12.391 r_dihedral_angle_1_deg 5.515 r_scangle_it 2.103 r_scbond_it 1.301 r_angle_refined_deg 1.131 r_angle_other_deg 0.897 r_mcangle_it 0.821 r_mcbond_it 0.507 r_nbd_refined 0.196 r_nbd_other 0.177 r_nbtor_refined 0.168 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_other 0.109 r_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 8543 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing