☰ Navigation Tabs
Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 15% (w/v) PEG8000, 0.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.275 α = 90 b = 102.445 β = 90 c = 188.919 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 2.09 50 99.6 0.09 13 4.5 110896
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.21
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 1LI4 2.09 48.14 108795 2101 99.56 0.2107 0.2103 0.2158 0.2308 0.2309 RANDOM 42.602
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] 2.27 2.2 -4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 15.448 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 6.31 r_angle_refined_deg 1.563 r_angle_other_deg 0.979 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 15.448 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 6.31 r_angle_refined_deg 1.563 r_angle_other_deg 0.979 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13320 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 276
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction