☰ Navigation Tabs
Biosynthetic thiolase from Clostridium kluyveri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 20% PEG 3350 and 0.2M Ammonium iodide
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.568 α = 90 b = 73.568 β = 90 c = 273.996 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 CCD ADSC QUANTUM 270 2015-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 46.7 97.78 0.03003 0.04246 0.03003 0.999 20.85 2 58118 28.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 82.77 0.3493 0.494 0.3493 0.663 1.9 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 46.65 56112 2011 97.79 0.20962 0.20853 0.2179 0.23954 0.2445 RANDOM 32.901
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] 0.28 0.14 0.28 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.939 r_dihedral_angle_2_deg 7.399 r_dihedral_angle_1_deg 6.827 r_long_range_B_refined 5.561 r_long_range_B_other 5.561 r_scangle_other 5.007 r_scbond_it 3.318 r_scbond_other 3.317 r_mcangle_it 3.285 r_mcangle_other 3.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.939 r_dihedral_angle_2_deg 7.399 r_dihedral_angle_1_deg 6.827 r_long_range_B_refined 5.561 r_long_range_B_other 5.561 r_scangle_other 5.007 r_scbond_it 3.318 r_scbond_other 3.317 r_mcangle_it 3.285 r_mcangle_other 3.285 r_mcbond_it 2.42 r_mcbond_other 2.42 r_angle_refined_deg 1.407 r_angle_other_deg 0.475 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5686 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing