☰ Navigation Tabs
Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 Na-acetate, ammoniumacetate, PEG 3350, PEG400 as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 3.5 64.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.045 α = 90 b = 109.792 β = 90 c = 192.957 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 90 CCD RAYONIX MX-225 2011-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.314 96.478 87.5 0.182 0.215 0.112 4.5 3.5 307932 307932
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.38 45.8 7.317 7.317 9.335 5.693 0.1 2.3 23267
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 FREE R-VALUE 2PH5 1.49 9.996 1.33 237910 11959 98.56 0.1924 0.1906 0.1961 0.2254 0.2289 31.2906
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 15.134 f_angle_d 1.413 f_chiral_restr 0.081 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7414 Nucleic Acid Atoms Solvent Atoms 1035 Heterogen Atoms 92
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing ARP model building PDB_EXTRACT data extraction PHENIX refinement