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Crystal structure of Leu65 to Arg mutant of Diphthine synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WNG PDB ENTRY 1WNG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.8 295 3.85M Na Formate, 0.1M acetate, pH 5.8, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.197 α = 90 b = 104.197 β = 90 c = 137.827 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS V 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 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 1.9 30 99.9 0.068 0.065 20.3 9.4 60256 60256 25.6
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 1.9 1.97 100 0.368 0.349 6.43 9.5 5913
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 1WNG 1.9 30 60169 60169 3022 99.7 0.22 0.219 0.219 0.2171 0.234 0.2327 RANDOM 37.4
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] -1.36 -1.36 2.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.97 c_mcangle_it 2.06 c_scbond_it 1.97 c_mcbond_it 1.34 c_angle_deg 1.3 c_improper_angle_d 0.75 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4178 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 43
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling