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Crystal structure of Lys49 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 6.5 295 1.8M AMMONIUM SULFATE, 0.1M MES, 0.01M Co CHLORIDE , pH 6.5, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.17 61.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.501 α = 90 b = 104.501 β = 90 c = 137.523 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 2006-10-05 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 1.5 30 99.9 0.083 0.08 13.9 10.7 121413 121413 -3 -3 22.4
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 1.5 1.55 100 0.399 0.38 5.65 10.6 12000
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 1.5 30 121327 121327 6078 99.6 0.197 0.196 0.196 0.1975 0.206 0.2081 RANDOM 22.3
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.6 c_scbond_it 1.76 c_mcangle_it 1.51 c_angle_deg 1.4 c_mcbond_it 0.99 c_improper_angle_d 0.85 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.6 c_scbond_it 1.76 c_mcangle_it 1.51 c_angle_deg 1.4 c_mcbond_it 0.99 c_improper_angle_d 0.85 c_bond_d 0.006 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 4168 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 115
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing