☰ Navigation Tabs
Crystal structure of the PLP-bound C-S lyase in the external aldimine form from Staphylococcus hominis complexed with an inhibitor, L-cycloserine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298.15 4% Tacsimate pH 6.0, 12% PEG 3,350
(F1: PEG/ION HT, Hampton Research), 20mM L-cycloserine
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.466 α = 90 b = 115.456 β = 90 c = 118.962 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 120 PIXEL DECTRIS PILATUS3 6M 2018-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.42 52.88 99.6 0.103 0.11 0.039 0.997 9.8 7.9 143873
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 1.42 1.44 99.1 2.503 2.673 0.929 0.331 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DQ6 1.42 51.99 136702 7085 99.5 0.1921 0.1907 0.2189 0.2309 RANDOM 22.723
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] 0.08 1.11 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 7.169 r_angle_refined_deg 1.625 r_angle_other_deg 1.057 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 7.169 r_angle_refined_deg 1.625 r_angle_other_deg 1.057 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6341 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 44
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing