☰ Navigation Tabs
Crystal structure of MasL, a thiolase from Massilia sp. YMA4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 2% (v/v) Tacsimate pH 7.0, 16% (w/v) polyethylene glycol 3,350, and 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.786 α = 79.77 b = 76.995 β = 79 c = 98.082 γ = 62.98
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 RAYONIX MX300HE 2020-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.78 30 92.3 0.045 23.8 3.8 161164
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 1.78 1.84 0.233 5
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 4N44 1.78 29.9 152933 7924 92.02 0.1307 0.1282 0.1452 0.1804 0.193 RANDOM 21.674
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] 0.76 0.23 0.35 -0.09 -0.03 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.388 r_dihedral_angle_4_deg 16.558 r_dihedral_angle_3_deg 13.89 r_dihedral_angle_1_deg 6.562 r_rigid_bond_restr 1.785 r_angle_refined_deg 1.455 r_angle_other_deg 1.448 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.388 r_dihedral_angle_4_deg 16.558 r_dihedral_angle_3_deg 13.89 r_dihedral_angle_1_deg 6.562 r_rigid_bond_restr 1.785 r_angle_refined_deg 1.455 r_angle_other_deg 1.448 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11522 Nucleic Acid Atoms Solvent Atoms 1659 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction