☰ Navigation Tabs
The holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OVM PDB ENTRY 1OVM
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 34.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.603 α = 90 b = 108.421 β = 90 c = 146.593 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 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 56.17 92.4 0.07 11.3 3.8 127559 6 18
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 1.6 1.69 63.8 0.48 2.2 2.7
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 1OVM 1.6 30 121047 6436 92.2 0.165 0.163 0.17 0.2 0.2062 RANDOM 14.89
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] -0.61 -0.34 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.851 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 5.557 r_scangle_it 2.532 r_scbond_it 1.853 r_mcangle_it 1.66 r_mcbond_it 1.472 r_angle_refined_deg 1.207 r_angle_other_deg 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.851 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 5.557 r_scangle_it 2.532 r_scbond_it 1.853 r_mcangle_it 1.66 r_mcbond_it 1.472 r_angle_refined_deg 1.207 r_angle_other_deg 0.891 r_symmetry_vdw_refined 0.32 r_nbd_refined 0.204 r_symmetry_vdw_other 0.183 r_nbd_other 0.182 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.082 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 8564 Nucleic Acid Atoms Solvent Atoms 1109 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing