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PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INL pdb entry 1INL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 291 calcium chloride, PEG400, pH 7.5, microbatch, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.639 α = 90 b = 110.821 β = 90 c = 49.256 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 93 IMAGE PLATE RIGAKU RAXIS IV confocal 2001-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 30 90.9 0.048 36 44968 -3 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 47.1 0.193 7
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 AUTOMATED MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1INL 1.798 72.55 42629 42629 2272 90.69 0.20655 0.20655 0.20482 0.2139 0.24156 0.2529 RANDOM 22.253
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] -0.55 0.79 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.156 r_scangle_it 2.025 r_scbond_it 1.188 r_angle_refined_deg 1.008 r_mcangle_it 0.845 r_angle_other_deg 0.718 r_mcbond_it 0.447 r_symmetry_vdw_other 0.313 r_nbd_other 0.221 r_nbd_refined 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.156 r_scangle_it 2.025 r_scbond_it 1.188 r_angle_refined_deg 1.008 r_mcangle_it 0.845 r_angle_other_deg 0.718 r_mcbond_it 0.447 r_symmetry_vdw_other 0.313 r_nbd_other 0.221 r_nbd_refined 0.173 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.076 r_symmetry_vdw_refined 0.066 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4326 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing EPMR phasing REFMAC refinement