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Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaryl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP co-crystallized with substrate analogon glutaryl-CoA, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.01 69.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.472 α = 90 b = 156.472 β = 90 c = 141.403 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE MAR scanner 345 mm plate 2008-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.594 70.711 98.7 0.103 0.103 6.738 6.5 61822
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.73 91.4 0.455 0.455 1.7 6.1 8274
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 1PIX 2.6 68.52 61000 700 99.47 0.18934 0.18911 0.1874 0.20891 0.1829 RANDOM 36.737
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] -0.3 -0.15 -0.3 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 15.597 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 5.476 r_scangle_it 1.563 r_angle_refined_deg 1.144 r_scbond_it 0.945 r_mcangle_it 0.825 r_mcbond_it 0.476 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 15.597 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 5.476 r_scangle_it 1.563 r_angle_refined_deg 1.144 r_scbond_it 0.945 r_mcangle_it 0.825 r_mcbond_it 0.476 r_nbtor_refined 0.302 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8692 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 112
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection