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Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MJF PDB ENTRY 1MJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.5 295 30%(v/v) PEG 200, 0.1M acetate buffer, 0.1M NaCl, pH 4.5, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.24 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.411 α = 90 b = 122.735 β = 117.69 c = 102.085 γ = 90
Symmetry Space Group C 1 2 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 CCD RIGAKU JUPITER 210 2006-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30 99.7 0.072 0.052 8.5 4.9 108624 108624 18.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 98.3 0.413 0.342 2.29 4.7 10660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1MJF 2 30 108624 108624 5449 99.3 0.195 0.194 0.194 0.194 0.215 0.2167 RANDOM 39.8
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] 15.93 5.88 -6.7 -9.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 3.2 c_scbond_it 2.11 c_mcangle_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.26 c_improper_angle_d 0.78 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 3.2 c_scbond_it 2.11 c_mcangle_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.26 c_improper_angle_d 0.78 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8862 Nucleic Acid Atoms Solvent Atoms 827 Heterogen Atoms 82
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing