☰ Navigation Tabs
Crystal structure of the tri-functional malyl-CoA lyase from Roseiflexus castenholzii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 The protein sample was mixed with an equal volume of the reservoir solution (16 % (v/v) PEG3350 and 0.2 M sodium chloride), and the mixture was equilibrated against the reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.033 α = 90 b = 133.417 β = 90 c = 139.595 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 QUANTUM 315r 2018-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97893 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 50 96.6 0.097 0.047 0.987 7.3 4.6 73219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 97.9 0.387 0.186 0.905
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4L7Z 2.527 48.225 1.36 73110 3613 95.08 0.1784 0.1756 0.1796 0.2337 0.234 50.0814
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.024 f_angle_d 0.926 f_chiral_restr 0.052 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16016 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing