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Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 0.1 M MES pH 6.0, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.64 α = 90 b = 63.82 β = 92.72 c = 73.5 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 4M 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.18 48.17 99 0.0721 0.083 0.997 16.18 4.2 27391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.27 0.226 0.261 0.956
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 4YUV 2.18 48.17 26118 1375 98.3 0.1441 0.1416 0.1911 0.1948 RANDOM 17.36
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] 1.21 0.43 -0.07 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.971 r_dihedral_angle_4_deg 22.329 r_dihedral_angle_3_deg 14.88 r_dihedral_angle_1_deg 7.423 r_angle_other_deg 2.618 r_angle_refined_deg 2.489 r_mcangle_it 2.093 r_mcbond_other 1.263 r_mcbond_it 1.262 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.971 r_dihedral_angle_4_deg 22.329 r_dihedral_angle_3_deg 14.88 r_dihedral_angle_1_deg 7.423 r_angle_other_deg 2.618 r_angle_refined_deg 2.489 r_mcangle_it 2.093 r_mcbond_other 1.263 r_mcbond_it 1.262 r_chiral_restr 0.127 r_bond_other_d 0.035 r_gen_planes_other 0.032 r_bond_refined_d 0.023 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4411 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing